Contacts of the helix formed by residues 88 - 110 (chain A) in PDB entry 1YC9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 2.7 28.3 + - - +
87A HIS* 1.3 82.1 - - - +
89A PRO* 1.3 74.9 - - - +
90A SER* 3.9 6.0 + - - -
91A LEU* 3.2 14.4 + - - +
92A CYS* 3.0 25.1 + - - -
185A ILE* 4.9 2.6 - - - +
265A LEU 5.0 2.9 + - - -
266A VAL 3.8 19.5 - - - -
267A GLY* 4.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 5.9 1.3 - - + +
88A SER* 1.3 87.8 - - - +
90A SER* 1.3 58.0 + - - +
92A CYS* 3.2 6.6 + - + +
93A MET* 2.9 40.6 + - + +
267A GLY* 3.6 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.3 5.6 + - - -
89A PRO* 1.3 79.4 - - - +
91A LEU* 1.3 62.0 + - - +
93A MET* 3.6 9.2 + - - +
94A ALA* 3.2 23.2 + - - +
97A ARG* 4.6 2.8 + - - -
181A ALA* 5.5 0.2 - - - +
184A MET* 6.0 3.8 - - - +
185A ILE* 3.9 25.1 - - - +
265A LEU 5.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 3.6 4.3 - - - +
85A LEU* 3.2 37.0 - - + +
86A GLN 3.2 25.4 - - - +
87A HIS* 3.7 5.6 - - - +
88A SER* 3.2 21.3 + - - +
90A SER* 1.3 79.2 - - - +
92A CYS* 1.3 62.5 + - - +
94A ALA* 3.1 9.3 + - + +
95A MET* 3.0 52.1 + - + +
182A ARG* 6.5 0.4 - - + -
185A ILE* 3.7 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.0 30.1 - - - -
88A SER 3.0 23.8 + - - +
89A PRO* 3.9 6.5 - - + +
91A LEU* 1.3 77.4 - - - +
93A MET* 1.3 57.0 + - + +
95A MET* 3.4 29.1 + - + +
96A ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 2.9 27.3 + - + +
90A SER* 3.9 7.9 - - - +
92A CYS* 1.3 76.7 - - + +
94A ALA* 1.3 58.6 + - - +
96A ALA* 3.3 6.4 + - - +
97A ARG* 2.9 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 3.2 9.9 + - - +
91A LEU* 3.1 13.8 + - + +
93A MET* 1.3 79.3 - - - +
95A MET* 1.3 61.0 + - + +
97A ARG* 3.4 15.8 + - - +
98A LEU* 3.1 22.3 + - - +
178A SER* 4.7 12.4 - - - +
181A ALA* 3.5 32.3 - - + -
185A ILE* 5.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN 5.4 1.3 - - - +
87A HIS* 5.6 2.0 - - + -
91A LEU* 3.0 41.0 + - + +
92A CYS* 3.5 47.1 - - + +
94A ALA* 1.3 74.0 - - + +
96A ALA* 1.3 57.5 + - - +
98A LEU* 3.3 9.1 + - - +
99A LYS* 3.0 28.1 + - - +
178A SER* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A CYS 2.9 17.1 + - - +
93A MET* 3.6 8.3 - - - +
95A MET* 1.3 77.5 - - - +
97A ARG* 1.3 57.3 + - + +
99A LYS* 3.2 9.8 + - - +
100A GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 4.6 2.8 + - - -
93A MET* 2.9 55.7 + - + +
94A ALA* 3.6 28.9 - - - +
96A ALA* 1.3 74.1 - - + +
98A LEU* 1.3 64.4 + - - +
100A GLY* 3.7 2.0 + - - +
101A ALA* 3.4 19.2 + - - +
174A ALA* 4.7 3.6 - - - +
181A ALA* 4.5 8.7 - - - +
184A MET* 5.2 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 3.1 12.6 + - - +
95A MET* 3.6 11.2 - - - +
96A ALA 3.2 0.2 - - - -
97A ARG* 1.3 74.3 - - - +
99A LYS* 1.3 65.4 + - - +
101A ALA* 3.1 4.4 + - - +
102A GLN* 3.0 39.0 + - - +
171A LEU* 4.1 11.4 - - + -
174A ALA* 4.0 8.1 - - + +
175A GLU* 3.8 39.9 - - + +
178A SER* 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET 3.0 16.3 + - - +
96A ALA* 3.2 8.0 + - - +
98A LEU* 1.3 75.7 - - - +
100A GLY* 1.3 57.4 + - - +
102A GLN* 3.1 20.9 + - + +
103A GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 2.9 15.9 + - - -
97A ARG* 3.7 3.6 + - - -
98A LEU 3.1 0.4 - - - -
99A LYS* 1.3 76.9 - - - +
101A ALA* 1.3 56.4 + - - +
103A GLY* 3.2 3.2 + - - -
104A PHE* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG 3.4 8.4 + - - +
98A LEU 3.1 7.7 + - - +
100A GLY* 1.3 75.8 - - - +
102A GLN* 1.3 57.7 + - - +
104A PHE* 3.7 8.8 - - - +
105A ALA* 2.9 30.0 + - - +
167A ALA 5.2 0.5 - - - +
170A GLU* 4.7 3.1 - - + +
171A LEU* 3.9 14.9 - - + +
174A ALA* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.0 37.8 + - - +
99A LYS* 3.3 25.2 - - + +
101A ALA* 1.3 76.8 - - - +
103A GLY* 1.3 56.1 + - - +
105A ALA* 3.2 5.3 + - - +
106A ARG* 2.9 28.3 + - - +
171A LEU* 3.7 23.1 - - + +
175A GLU* 5.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS 2.9 13.5 + - - -
100A GLY* 3.2 4.5 + - - -
102A GLN* 1.3 74.7 - - - +
104A PHE* 1.3 55.7 + - - +
106A ARG* 3.4 8.2 + - - +
107A GLN* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY 2.9 16.2 + - - +
101A ALA* 3.7 9.0 - - - +
103A GLY* 1.3 75.2 - - - +
105A ALA* 1.3 58.2 - - - +
107A GLN* 3.2 23.9 + - + +
108A ALA* 2.9 31.6 + - + +
167A ALA* 3.9 32.1 - - + -
170A GLU* 5.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA 2.9 17.2 + - - +
102A GLN 3.6 4.5 - - - +
104A PHE* 1.3 77.7 - - - +
106A ARG* 1.3 61.4 + - - +
108A ALA* 3.3 2.3 + - - +
109A GLY* 3.0 21.1 + - - -
164A VAL* 5.6 1.9 - - - +
167A ALA* 4.1 27.4 - - - +
168A THR* 4.9 8.7 - - + +
171A LEU* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN 2.9 13.1 + - - +
103A GLY* 3.5 11.9 - - - +
105A ALA* 1.3 78.7 - - - +
107A GLN* 1.4 65.0 + - + +
109A GLY* 3.4 7.7 + - - -
110A ALA* 3.4 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY 3.0 23.6 + - - +
104A PHE* 3.2 26.7 + - + +
106A ARG* 1.4 76.0 - - + +
108A ALA* 1.3 63.1 + - - +
110A ALA* 3.2 22.6 - - - +
111A ILE* 4.1 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 2.9 21.4 + - + +
105A ALA 3.6 1.3 - - - +
107A GLN* 1.3 76.0 - - - +
109A GLY* 1.3 64.2 + - - +
111A ILE* 3.0 30.2 + - - +
163A ALA* 4.6 9.0 - - + +
164A VAL* 3.6 4.6 - - + +
167A ALA* 3.3 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.0 14.4 + - - -
106A ARG* 3.4 4.7 + - - -
107A GLN 3.4 0.4 - - - -
108A ALA* 1.3 76.0 - - - +
110A ALA* 1.4 61.2 + - - +
112A ARG* 3.1 20.4 + - - +
113A SER* 3.9 3.1 + - - -
164A VAL* 3.8 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ARG 3.4 8.1 + - - +
107A GLN* 3.2 19.6 + - - +
108A ALA 3.1 0.4 - - - -
109A GLY* 1.4 75.8 - - - +
111A ILE* 1.3 61.6 + - - +
112A ARG 3.1 1.0 + - - -
113A SER* 3.1 29.2 + - - +
115A ASP* 4.6 7.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il