Contacts of the helix formed by residues 94 - 112 (chain A) in PDB entry 3RIG
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 ASN 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA* 2.9 15.8 + - + +
93A HIS* 1.3 81.0 - - + +
95A PRO* 1.3 71.8 - - - +
96A SER* 3.0 11.5 + - - +
97A ARG* 3.1 66.9 + - + +
98A VAL* 3.3 9.1 + - + +
196A ASP* 5.1 2.0 + - - +
198A SER* 6.0 0.4 - - - +
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Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.2 43.3 - - + +
92A ALA 4.2 4.7 - - - +
93A HIS 3.7 3.6 - - - +
94A ASN* 1.3 90.0 - - - +
96A SER* 1.3 57.2 + - - +
98A VAL* 3.4 1.8 + - + +
99A TRP* 2.9 33.8 + - - +
201A VAL* 4.8 9.0 - - + -
204A LEU* 3.8 20.0 - - + -
215A LEU* 4.3 11.2 - - + -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN* 3.0 9.7 + - - +
95A PRO* 1.3 77.6 - - - +
97A ARG* 1.3 60.6 + - - +
99A TRP* 3.3 2.1 + - - +
100A GLU* 2.8 31.7 + - - +
184A LEU* 5.3 0.2 - - - +
197A ALA* 4.2 4.2 - - - +
198A SER* 3.5 14.5 + - - -
199A ILE* 2.8 49.2 + - - +
204A LEU* 3.8 12.8 - - - +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 3.9 16.6 - - + -
80A TRP* 3.1 54.2 - - - +
85A LEU* 4.2 14.1 - - + -
94A ASN* 3.1 51.2 + - + +
96A SER* 1.3 77.4 - - - +
98A VAL* 1.3 58.4 + - + +
100A GLU* 3.2 8.7 + - - +
101A PHE* 3.0 27.3 + - - +
196A ASP* 3.1 39.9 + - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.7 19.3 - - + +
90A ALA* 3.6 45.3 - - + +
91A PHE* 3.7 24.0 - - + +
94A ASN* 3.3 3.5 + - + +
95A PRO 3.8 6.5 - - - +
96A SER 3.3 0.6 - - - -
97A ARG* 1.3 76.7 - - + +
99A TRP* 1.3 58.6 + - - +
101A PHE* 3.2 6.9 + - - +
102A TYR* 2.9 53.2 + - + -
218A PRO* 5.2 1.3 - - + -
222A TRP* 4.0 9.0 - - + -
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Residues in contact with TRP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.7 21.0 - + - -
95A PRO 2.9 16.4 + - - +
96A SER 3.9 3.1 - - - +
98A VAL* 1.3 73.4 - - - +
100A GLU* 1.3 57.0 + - - +
102A TYR* 4.1 11.9 - - + -
103A HIS* 2.7 37.2 + - - +
106A ARG* 4.2 15.0 - - - -
161A LEU 6.0 0.2 - - - -
164A THR* 4.5 3.6 - - + -
180A ILE* 3.6 32.1 - - + -
184A LEU* 3.9 16.1 - - + +
204A LEU* 4.0 24.7 - - + -
205A PRO* 3.8 31.3 - - + +
215A LEU* 4.5 0.6 - - + +
216A LEU* 2.8 28.1 + - + -
217A ARG 3.7 9.4 - - - -
218A PRO* 3.6 37.5 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 3.9 10.7 - - + -
78A ARG* 2.9 34.4 + - - -
96A SER* 2.8 19.4 + - - +
97A ARG* 3.2 7.1 + - - +
99A TRP* 1.3 76.5 - - - +
101A PHE* 1.3 59.7 + - - +
103A HIS* 3.6 1.1 - - - +
104A TYR* 3.0 24.1 + - - +
184A LEU* 3.9 18.6 - - + +
187A LYS* 3.5 8.6 - - + +
188A GLY* 2.9 26.8 + - - -
195A GLN 4.5 1.2 - - - +
196A ASP* 3.5 4.5 - - - +
197A ALA* 2.6 46.5 + - + +
198A SER 4.7 0.3 + - - -
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 3.6 51.5 - + + -
82A ALA* 4.2 12.3 - - + -
85A LEU* 3.7 28.9 - - + -
97A ARG 3.0 12.4 + - - +
98A VAL* 3.5 8.5 - - - +
100A GLU* 1.3 77.7 - - - +
102A TYR* 1.3 86.0 + + - +
104A TYR* 3.1 7.6 + + - +
105A ARG* 3.0 51.3 + - + +
2001A NHE 3.6 37.0 - - + -
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU 4.5 3.8 - - - -
86A ALA* 3.2 11.8 - - - +
98A VAL* 2.9 43.0 + - + +
99A TRP* 4.1 9.0 - - + -
101A PHE* 1.3 88.4 - + - +
103A HIS* 1.3 61.2 + - - +
105A ARG* 3.7 2.7 - - + +
106A ARG* 2.8 40.1 + - - +
142A ILE* 4.2 4.0 - - + -
161A LEU* 3.5 24.5 - - + -
218A PRO* 3.6 31.4 - - + -
220A VAL* 4.0 5.8 - - + +
222A TRP* 3.0 33.2 + + - -
2001A NHE 2.5 41.4 + - - -
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 2.7 25.0 + - + +
100A GLU 3.6 3.6 - - - +
102A TYR* 1.3 72.8 - - - +
104A TYR* 1.3 63.2 + - - +
106A ARG* 3.2 10.5 + - - +
107A GLU* 2.9 64.8 + - + +
179A PRO* 3.7 26.5 - - + +
180A ILE* 4.4 8.9 + - + +
184A LEU* 3.2 44.5 + - + +
186A GLY* 4.5 4.0 + - - -
187A LYS* 3.5 25.1 + - + -
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR 6.2 0.2 - - - -
77A TRP* 3.4 25.4 - + + +
100A GLU 3.0 11.4 + - - +
101A PHE* 3.2 10.3 - + - +
103A HIS* 1.3 77.2 - - - +
105A ARG* 1.3 75.9 + - + +
107A GLU* 3.0 8.5 + - + +
108A VAL* 2.8 57.6 + - + +
187A LYS 5.5 0.2 - - - -
188A GLY* 3.3 30.3 - - - +
189A ALA* 5.0 0.4 - - - -
190A PRO* 3.7 34.1 - - + +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.0 49.9 + - + +
102A TYR* 3.8 5.8 - - + +
103A HIS 3.3 0.2 - - - -
104A TYR* 1.3 89.3 - - + +
106A ARG* 1.3 57.3 + - - +
108A VAL* 4.7 3.1 - - - -
109A MET* 2.8 81.3 + - - +
141A ASN* 5.8 4.0 - - - +
142A ILE* 3.9 16.8 - - - +
143A ASP* 5.6 2.0 - - - +
161A LEU* 3.8 20.9 - - + +
2001A NHE 2.6 39.7 + - - +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TRP* 4.2 16.8 - - - -
102A TYR* 2.8 30.1 + - - +
103A HIS* 3.6 7.5 + - - +
105A ARG* 1.3 76.3 - - - +
107A GLU* 1.3 65.2 + - - +
110A GLY* 2.8 31.4 + - - -
161A LEU* 2.9 42.8 + - + +
162A PHE* 3.8 21.3 - - + +
163A LYS 4.8 0.2 - - - +
164A THR* 5.2 1.6 - - - +
175A ASN* 2.7 42.6 + - - +
176A TYR 3.8 3.0 - - - -
177A LYS 2.8 31.5 + - - +
180A ILE* 3.7 26.6 - - - +
218A PRO* 6.3 0.4 - - - -
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A HIS* 2.9 54.4 + - + +
104A TYR* 3.6 8.5 - - + +
106A ARG* 1.3 85.3 + - - +
108A VAL* 1.3 65.7 + - + +
110A GLY* 4.2 0.3 - - - -
111A SER* 3.6 17.7 + - - -
177A LYS 5.0 1.0 - - - +
178A SER* 3.1 33.9 + - - -
179A PRO* 4.4 0.6 - - - +
180A ILE 5.1 0.2 + - - -
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 2.8 56.9 + - + +
105A ARG* 4.0 3.6 - - - +
107A GLU* 1.3 73.3 - - + +
109A MET* 1.3 78.9 + - + +
111A SER* 2.6 25.3 + - - -
112A LYS* 3.6 33.6 + - - +
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Residues in contact with MET 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 5.9 1.1 - - - -
105A ARG* 2.8 55.8 + - - +
108A VAL* 1.3 87.5 - - + +
110A GLY* 1.3 63.6 + - - +
112A LYS* 3.0 40.6 + - - +
143A ASP* 4.1 26.8 - - + +
145A LEU* 5.1 5.4 - - - +
148A LYS* 4.7 3.5 + - - -
161A LEU* 3.7 19.1 - - + -
162A PHE* 4.2 7.9 - - + -
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG 2.8 24.4 + - - -
107A GLU 4.2 0.7 - - - -
108A VAL 3.4 0.2 - - - -
109A MET* 1.3 72.9 - - - +
111A SER* 1.3 58.8 + - - +
112A LYS 3.7 0.7 + - - +
148A LYS* 3.8 17.7 + - - -
162A PHE* 3.7 17.4 - - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU 3.6 10.8 + - - -
108A VAL* 2.6 23.3 + - - -
110A GLY* 1.3 76.8 - - - +
112A LYS* 1.3 69.9 + - - +
113A GLU* 3.6 8.5 + - - +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL 6.0 1.8 - - - +
108A VAL* 3.7 37.2 + - - +
109A MET* 3.0 33.4 + - - +
110A GLY 4.4 0.2 - - - +
111A SER* 1.3 83.3 + - - +
113A GLU* 1.3 65.5 + - - +
145A LEU* 3.6 30.0 - - + +
148A LYS* 3.7 14.9 + - - +
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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
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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) + - + + + + + -
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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