Contacts of the helix formed by residues 86 - 100 (chain A) in PDB entry 2X5N
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 LYS 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 2.8 16.3 + - - +
57A ASN* 3.7 34.5 - - - +
59A PRO* 3.7 18.4 - - + +
84A ASN* 4.2 26.7 - - - +
85A ALA* 1.3 79.2 - - - +
87A PHE* 1.3 64.1 + - - +
88A GLY 3.5 2.0 - - - -
89A ASP* 3.5 19.7 + - + +
90A GLY* 2.9 19.1 + - - -
119A VAL* 4.3 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 6.3 0.4 - - + -
54A ILE* 4.2 20.5 - - + +
85A ALA* 3.8 4.1 + - + +
86A LYS* 1.3 73.7 - - - +
88A GLY* 1.3 62.7 + - - +
90A GLY* 3.1 2.8 + - - -
91A ILE* 2.9 61.2 + - + +
112A ALA* 4.4 5.4 - - + -
114A VAL* 3.7 31.0 - - + -
118A ILE* 4.1 26.7 - - + -
119A VAL* 4.3 2.0 - - - +
120A GLU* 3.9 7.3 + - - +
125A LEU* 3.6 32.1 - - + -
128A LEU* 4.9 2.0 - - + -
141A ILE* 3.8 22.9 - - + -
153A LEU* 4.7 5.4 - - + -
156A PHE* 4.1 16.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 1.3 71.8 - - - +
89A ASP* 1.3 66.1 + - - +
91A ILE* 3.3 3.1 + - - +
92A GLN* 3.0 32.1 + - - +
120A GLU* 2.9 33.3 + - - -
128A LEU* 3.8 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 4.0 16.7 - - + +
86A LYS* 3.5 26.1 + - + +
87A PHE 3.4 0.2 - - - -
88A GLY* 1.3 75.2 - - - +
90A GLY* 1.3 57.2 + - - +
92A GLN* 3.3 13.9 + - - +
93A ILE* 2.9 39.2 + - + +
120A GLU* 4.0 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.7 6.7 - - - +
52A MET* 3.4 6.7 - - - +
54A ILE* 4.0 12.3 - - - -
59A PRO* 3.6 19.3 - - - +
86A LYS 2.9 15.3 + - - -
87A PHE 3.1 3.8 + - - -
89A ASP* 1.3 77.9 - - - +
91A ILE* 1.3 55.2 + - - +
93A ILE 3.4 0.5 + - - -
94A ALA* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.2 8.1 - - + -
87A PHE* 2.9 49.3 + - + +
88A GLY* 3.6 9.0 - - - +
90A GLY* 1.3 74.3 - - - +
92A GLN* 1.3 61.8 + - - +
94A ALA* 3.4 5.1 + - - +
95A GLN* 3.1 39.7 + - - +
110A ILE* 3.7 14.4 - - + +
112A ALA* 4.6 1.1 - - + -
128A LEU* 4.6 15.3 - - + -
132A MET* 3.8 20.0 - - + -
139A ILE* 3.4 30.1 - - + -
156A PHE* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY 3.0 18.6 + - - +
89A ASP* 3.7 14.6 - - - +
91A ILE* 1.3 74.9 - - - +
93A ILE* 1.3 65.3 + - + +
95A GLN* 3.1 16.0 + - - +
96A LEU* 3.1 20.3 + - - +
128A LEU* 3.7 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A MET* 3.6 22.7 - - + -
58A SER* 6.1 0.2 - - - +
59A PRO* 4.0 34.8 - - + +
61A VAL* 4.3 15.3 - - + +
89A ASP* 2.9 25.3 + - + +
92A GLN* 1.3 76.0 - - + +
94A ALA* 1.3 57.0 + - - +
96A LEU* 3.1 16.1 + - + +
97A ALA* 2.9 27.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
7A MET* 3.9 5.5 - - + +
9A LEU* 3.9 14.8 - - + -
52A MET* 3.6 19.2 - - - -
90A GLY 2.9 17.7 + - - +
91A ILE 3.5 6.5 - - - +
92A GLN 3.2 0.2 - - - -
93A ILE* 1.3 78.0 - - - +
95A GLN* 1.3 56.4 + - - +
97A ALA* 3.2 4.8 + - - +
98A LEU* 2.9 34.3 + - - +
110A ILE* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 3.1 26.2 + - - +
92A GLN* 3.1 16.0 + - - +
94A ALA* 1.3 76.8 - - - +
96A LEU* 1.3 62.8 + - - +
98A LEU* 3.3 8.2 + - - +
99A LYS* 3.2 31.4 + - - +
108A GLN* 4.5 2.9 - - - +
110A ILE* 4.1 11.2 - - + -
128A LEU* 5.2 2.0 + - - +
131A ARG* 5.4 3.8 - - - +
132A MET* 3.6 28.9 - - - +
135A ASN* 3.0 37.0 + - - +
137A VAL* 4.0 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN 3.1 11.7 + - - +
93A ILE* 3.4 18.2 - - + +
95A GLN* 1.3 77.3 - - - +
97A ALA* 1.3 62.5 + - - +
99A LYS* 3.1 35.2 + - + +
100A HIS* 3.7 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 4.2 26.9 - - + -
61A VAL* 4.7 15.3 - - + -
65A LEU* 5.0 3.9 - - - +
93A ILE 2.9 14.0 + - - +
94A ALA* 3.2 9.8 + - - +
96A LEU* 1.3 75.4 - - - +
98A LEU* 1.3 58.0 + - - +
100A HIS* 2.9 33.8 + - - +
101A ARG* 3.8 2.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
5A ALA* 3.5 41.3 - - + +
6A THR 4.4 0.4 - - - +
7A MET* 3.6 22.9 - - + +
65A LEU* 4.7 5.4 - - + -
94A ALA 2.9 21.7 + - - +
95A GLN* 3.7 5.4 - - - +
96A LEU 3.3 0.4 - - - -
97A ALA* 1.3 76.0 - - - +
99A LYS* 1.3 59.5 + - - +
101A ARG* 3.0 33.7 + - - +
108A GLN* 3.3 27.6 - - + +
109A ARG 3.7 24.7 - - - +
110A ILE* 4.0 14.6 - - + -
137A VAL* 4.4 5.8 - - + -
----------------------------------------------------------
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 GLN* 3.2 22.3 + - - +
96A LEU* 3.3 22.6 - - + +
97A ALA 3.1 0.6 - - - -
98A LEU* 1.3 76.7 - - - +
100A HIS* 1.3 66.0 + - + +
101A ARG* 3.2 8.3 - - - +
104A LYS* 3.4 23.1 - - - -
108A GLN* 5.0 4.7 - - - +
135A ASN* 6.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 5.2 0.4 - - - -
96A LEU* 3.7 37.9 + - + +
97A ALA* 2.9 17.1 + - - +
99A LYS* 1.3 80.2 - - + +
101A ARG* 1.3 66.9 + - - +
104A LYS* 4.6 2.5 + - - +
----------------------------------------------------------
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