Contacts of the helix formed by residues 91 - 106 (chain A) in PDB entry 2H4C
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 CYS 91 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.1 17.3 - - - -
58A ASP* 3.4 21.5 - - + -
59A CYS* 2.0 61.5 - - + -
89A ASN* 2.6 17.2 + - - +
90A LEU* 1.3 74.5 - - + +
92A LEU* 1.3 59.0 + - - +
93A LYS 3.1 1.6 - - - -
94A THR* 2.8 22.4 + - - -
95A VAL* 3.1 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A CYS* 4.8 10.5 - - + -
71A ALA* 4.8 12.8 - - + -
72A THR 3.9 18.6 - - - +
73A TYR* 3.5 21.6 - - + +
86A ASP* 3.6 32.4 - - + +
89A ASN* 2.7 53.8 + - + +
91A CYS* 1.3 77.3 - - + +
93A LYS* 1.3 59.8 + - - +
94A THR 3.1 0.7 + - - -
95A VAL* 3.8 7.6 + - - +
96A CYS* 3.5 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 5.5 2.0 - - - +
84A CYS* 3.0 40.3 + - + +
85A GLY* 5.0 0.6 - - - -
86A ASP* 3.2 28.1 + - - +
88A ASN 4.4 2.0 - - - +
89A ASN 2.9 11.8 + - - +
90A LEU* 4.0 11.4 - - - +
92A LEU* 1.3 76.8 - - - +
94A THR* 1.3 59.3 + - - +
96A CYS* 4.1 3.9 - - - +
97A GLU* 3.4 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS 5.2 0.4 - - - +
54A THR* 6.0 0.2 - - - +
55A VAL* 3.6 25.4 - - + -
90A LEU 2.8 21.5 + - - -
91A CYS* 2.8 12.0 + - - -
93A LYS* 1.3 77.5 - - - +
95A VAL* 1.3 67.0 + - - -
96A CYS 2.9 1.3 - - - -
97A GLU* 2.9 6.7 + - + +
98A CYS* 2.7 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN 4.6 0.7 - - - +
52A TYR* 4.2 13.9 - - + +
55A VAL* 4.4 4.9 - - + -
59A CYS* 3.8 17.9 - - - -
68A PRO* 3.6 46.4 - - + +
71A ALA* 3.9 13.0 - - + -
73A TYR* 4.0 21.1 - - + -
91A CYS 3.1 12.1 + - - +
92A LEU 4.2 4.5 - - - +
94A THR* 1.3 77.6 - - - +
96A CYS* 1.3 60.5 + - - +
98A CYS* 3.4 6.8 + - - +
99A ASP* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 5.1 3.4 - - - -
73A TYR* 3.3 43.9 - - + -
74A SER 4.3 0.2 - - - -
75A TYR* 4.0 8.3 - - - -
84A CYS* 2.0 51.1 - - + -
86A ASP* 5.1 0.4 - - - +
92A LEU 3.5 12.4 + - - +
93A LYS 4.1 1.6 - - - +
94A THR 2.9 0.2 - - - -
95A VAL* 1.3 77.6 - - - +
97A GLU* 1.3 55.2 + - - +
99A ASP* 3.1 1.9 + - - +
100A ARG* 2.5 39.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
84A CYS* 3.7 6.4 - - - +
93A LYS* 3.4 27.2 + - - +
94A THR* 2.9 9.9 + - + +
96A CYS* 1.3 77.4 - - - +
98A CYS* 1.3 58.6 + - - +
100A ARG* 2.8 49.1 + - - +
101A ALA* 2.9 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 4.1 5.4 - - + -
51A CYS* 2.0 67.1 - - + -
52A TYR* 4.1 15.3 - - + -
55A VAL* 4.8 1.6 - - - -
94A THR* 2.7 34.9 + - - +
95A VAL 3.6 4.7 - - - +
97A GLU* 1.3 73.6 - - - +
99A ASP* 1.3 58.5 + - - +
101A ALA* 3.8 3.5 - - - +
102A ALA* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASN 3.9 1.2 - - - +
5A PHE* 2.9 44.9 + - + +
8A MET* 3.8 5.4 - - - -
48A HIS* 2.9 6.8 + - - -
52A TYR* 2.6 41.5 + - - -
73A TYR* 3.1 27.6 + - - +
95A VAL 3.1 9.7 + - - +
96A CYS 3.1 5.7 + - - +
98A CYS* 1.3 74.5 - - - +
100A ARG* 1.3 64.0 + - - +
102A ALA* 3.0 4.2 - - - +
103A ALA* 2.9 23.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
8A MET* 3.0 23.8 - - + +
81A ASP* 5.4 1.2 + - - -
82A ILE* 3.7 32.1 + - + +
83A VAL* 5.4 0.2 - - - +
84A CYS* 4.2 13.2 - - - +
96A CYS 2.5 21.7 + - - +
97A GLU* 2.8 37.6 + - - +
99A ASP* 1.3 76.2 - - - +
101A ALA* 1.3 103.1 + - - +
103A ALA* 2.9 11.6 + - - +
104A ILE* 3.3 35.5 + - + +
----------------------------------------------------------
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 GLU* 2.9 21.6 + - + +
98A CYS* 3.8 3.6 - - - +
100A ARG* 1.3 88.9 - - - +
102A ALA* 1.3 50.6 + - - +
104A ILE* 2.7 30.7 + - - +
105A CYS* 2.7 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.3 25.6 - - + -
44A CYS* 5.9 2.2 - - + +
48A HIS* 3.8 17.7 - - + -
98A CYS 2.8 15.8 + - - +
99A ASP 3.0 13.0 - - - +
101A ALA* 1.3 75.4 - - - +
103A ALA* 1.3 53.9 + - - +
105A CYS* 3.0 11.2 + - - +
106A LEU* 2.8 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.3 0.2 - - - -
8A MET* 3.1 41.5 - - + +
9A ILE* 3.4 19.3 - - + +
12A MET* 2.9 29.7 - - + +
13A THR* 4.8 0.2 + - - -
82A ILE* 4.6 5.6 - - + -
99A ASP 2.9 13.7 + - - +
100A ARG 2.9 7.6 + - - +
102A ALA* 1.3 73.2 - - - +
104A ILE* 1.3 58.8 + - - +
106A LEU* 4.1 3.2 - - - +
107A GLY* 3.6 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 4.0 28.9 - - + -
82A ILE* 5.3 3.6 - - + +
100A ARG* 3.4 52.7 - - + +
101A ALA* 2.7 7.7 + - - +
103A ALA* 1.3 76.9 - - - +
105A CYS* 1.3 65.8 + - - +
106A LEU 3.3 0.2 - - - -
107A GLY* 3.6 1.3 - - - -
108A GLN* 3.2 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A CYS* 2.0 51.2 - - + -
47A VAL* 6.1 1.8 - - - -
101A ALA 2.7 11.1 + - - +
102A ALA* 3.1 14.8 - - - +
104A ILE* 1.3 80.4 - - - +
106A LEU* 1.3 60.1 + - - +
107A GLY 3.1 1.3 + - - -
109A ASN* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 4.6 8.1 - - + -
9A ILE* 3.4 50.0 - - + -
13A THR* 3.4 2.5 + - - -
22A TYR* 3.2 45.3 + - + +
41A THR* 3.9 14.3 + - + +
44A CYS* 3.9 23.1 - - + -
45A CYS* 4.4 6.7 - - - -
102A ALA* 2.8 19.3 + - + +
103A ALA* 4.6 1.1 - - - -
105A CYS* 1.3 74.3 - - - +
107A GLY* 1.3 57.4 + - - +
109A ASN* 4.2 3.1 - - - -
110A VAL* 2.9 26.6 + - - +
----------------------------------------------------------
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