Contacts of the helix formed by residues 92 - 104 (chain A) in PDB entry 3ESF
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 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 1.3 76.7 - - - +
93A GLY* 1.3 69.6 + - - +
94A LYS 3.5 0.3 + - - -
95A LEU* 3.9 3.3 + - - +
96A ALA* 3.6 12.9 + - - -
192A GLU* 3.4 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER* 1.3 77.2 - - - +
94A LYS* 1.3 62.2 + - - -
96A ALA* 3.3 3.6 + - - +
97A GLU* 3.2 25.6 + - - +
100A ARG* 5.1 0.2 + - - -
192A GLU* 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 3.5 0.8 + - - -
93A GLY* 1.3 70.7 - - - -
95A LEU* 1.3 58.2 + - - +
97A GLU* 3.5 6.3 + - - +
98A ALA* 3.0 28.2 + - - +
192A GLU* 4.4 11.7 + - + +
195A PHE* 3.7 18.7 - - + -
196A THR* 3.9 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 4.2 8.1 - - + -
92A SER 3.9 6.6 + - - +
93A GLY 3.4 0.2 - - - -
94A LYS* 1.3 77.8 - - - +
96A ALA* 1.3 60.1 + - - +
98A ALA* 3.2 0.9 + - - +
99A ILE* 2.9 42.7 + - + +
128A LEU* 5.2 1.1 - - + -
137A LEU* 4.2 15.3 - - + -
157A ILE* 4.7 9.4 - - + -
188A TRP* 3.9 21.8 - - + +
191A ALA* 3.6 31.9 - - + -
192A GLU* 3.8 21.6 + - + +
195A PHE* 3.7 37.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
91A PRO* 3.4 37.6 - - + +
92A SER* 3.6 18.8 + - - -
93A GLY 3.3 3.4 + - - +
95A LEU* 1.3 77.9 - - - +
97A GLU* 1.3 62.0 + - - +
99A ILE* 3.5 5.5 + - - +
100A ARG* 3.2 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY 3.2 14.2 + - - +
94A LYS* 3.8 6.5 - - - +
96A ALA* 1.3 77.8 - - - +
98A ALA* 1.3 59.0 + - - +
100A ARG* 3.0 44.1 + - - +
101A ALA* 2.9 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS 3.0 12.0 + - - +
95A LEU* 3.2 4.9 + - - +
97A GLU* 1.3 71.7 - - - +
99A ILE* 1.3 60.7 + - - +
101A ALA* 3.3 8.0 + - - +
102A SER* 3.0 33.3 + - - +
135A LYS 5.9 1.3 - - - +
137A LEU* 3.8 8.5 - - + -
195A PHE* 3.3 39.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 4.0 26.0 - - + -
95A LEU* 2.9 24.2 + - + +
96A ALA* 3.7 7.2 - - - +
97A GLU 3.3 0.2 - - - -
98A ALA* 1.3 75.7 - - - +
100A ARG* 1.3 54.4 + - + +
102A SER 3.2 0.5 + - - -
103A PHE* 2.8 46.2 + - + +
105A SER 4.1 0.9 - - - +
106A PHE* 4.0 24.9 - - + -
109A PHE* 3.8 42.0 - - + -
128A LEU* 4.4 8.3 - - + -
137A LEU* 3.9 17.3 - - + -
188A TRP* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 5.1 8.1 + - - -
93A GLY 5.1 0.4 + - - -
96A ALA* 3.2 36.4 + - - +
97A GLU* 3.0 46.7 + - - +
99A ILE* 1.3 75.1 - - + +
101A ALA* 1.3 57.7 + - - +
104A GLY* 2.8 34.0 + - - +
105A SER* 4.1 24.2 - - - +
106A PHE* 4.5 9.6 - - + +
----------------------------------------------------------
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 GLU* 2.9 17.5 + - + +
98A ALA* 3.3 8.5 + - - +
100A ARG* 1.3 74.6 - - - +
102A SER* 1.3 59.2 + - - +
104A GLY 4.9 0.2 - - - -
136A LYS* 3.4 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA 3.0 15.7 + - - -
101A ALA* 1.3 77.6 - - - +
103A PHE* 1.3 69.1 + - - +
104A GLY 3.8 0.2 - - - -
135A LYS 4.8 0.9 + - - -
136A LYS* 3.6 17.8 - - - +
137A LEU* 2.8 50.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ILE* 2.8 33.8 + - + +
102A SER* 1.3 77.1 - - - +
104A GLY* 1.3 56.0 + - - +
105A SER 3.2 18.3 + - - +
108A LYS* 3.4 22.1 - - + +
109A PHE* 3.6 43.7 - + + +
112A GLU* 3.7 25.1 - - - -
128A LEU* 4.0 5.8 - - + -
137A LEU* 3.6 40.8 - - + -
138A LYS* 3.7 15.9 - - - -
139A VAL* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 2.8 26.6 + - - +
101A ALA 4.9 0.2 - - - -
102A SER 3.8 0.8 - - - -
103A PHE* 1.3 76.5 - - - +
105A SER* 1.3 61.9 + - - +
----------------------------------------------------------
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