Contacts of the helix formed by residues 104 - 113 (chain A) in PDB entry 3ZNG
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 THR 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A HIS* 3.7 3.6 - - - -
95A VAL 5.0 2.5 - - - -
96A ASN* 4.6 10.3 - - - +
97A GLY 3.5 11.4 - - - +
98A VAL* 3.8 19.5 - - + -
102A TRP 3.9 4.7 + - - +
103A HIS* 1.3 78.4 - - - +
105A PRO* 1.3 75.7 - - - +
106A LEU* 3.7 8.4 + - - +
107A PHE* 2.9 30.9 + - - +
108A ASN* 3.1 12.5 + - - -
127A SER 5.5 2.3 + - - -
130A PRO* 5.7 10.1 - - + +
135A ALA 5.6 0.3 + - - -
137A PRO* 4.7 5.7 - - - +
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Residues in contact with PRO 105 (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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73A LEU* 3.9 23.3 - - + +
74A HIS* 3.3 22.4 - - + +
77A CYS* 3.5 29.3 - - + +
94A GLN 4.0 4.3 - - - +
95A VAL 3.3 32.3 - - - +
97A GLY 3.3 15.7 - - - +
104A THR* 1.3 84.3 - - - +
106A LEU* 1.3 60.1 + - - +
108A ASN* 3.5 2.7 + - + -
109A ALA 3.1 18.2 + - - -
121A LEU* 3.5 9.6 - - + +
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Residues in contact with LEU 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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95A VAL 4.7 1.0 + - - +
96A ASN* 6.1 0.2 - - - +
104A THR* 3.1 9.2 + - - +
105A PRO* 1.3 77.1 - - - +
107A PHE* 1.3 67.6 + - - +
109A ALA* 3.4 1.6 + - - +
110A CYS* 3.2 18.7 + - - -
118A VAL* 4.0 42.4 - - + +
121A LEU* 3.7 12.2 - - + +
122A LEU* 3.9 17.9 - - + -
126A ALA* 4.2 13.7 - - + -
127A SER 3.5 25.6 - - - +
128A VAL* 4.3 1.3 - - - -
137A PRO* 4.3 14.4 - - + -
153A LEU* 3.7 23.3 - - + -
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Residues in contact with PHE 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* 3.6 32.8 - + - -
104A THR* 2.9 25.7 + - - +
106A LEU* 1.3 78.5 - - - +
108A ASN* 1.3 70.7 + - - +
110A CYS* 2.9 21.0 + - - +
111A VAL* 3.1 23.4 + - + +
134A LEU 4.6 4.9 - - - -
135A ALA* 3.6 41.1 - - + +
136A SER 4.0 2.5 - - - -
137A PRO* 3.8 23.0 - - + +
140A GLU* 3.6 39.0 - - + -
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Residues in contact with ASN 108 (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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74A HIS* 3.2 44.5 + - - +
75A GLU* 5.9 0.2 + - - -
77A CYS* 3.7 3.4 - - + +
78A LEU* 3.8 39.3 - - + +
99A THR* 5.6 0.6 - - - +
103A HIS* 3.7 17.7 + - - +
104A THR 3.1 5.7 + - - -
105A PRO 3.7 7.4 - - - +
107A PHE* 1.3 89.9 - - - +
109A ALA* 1.3 63.3 + - - +
111A VAL* 2.9 16.1 + - - +
112A SER* 2.9 14.2 + - - -
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Residues in contact with ALA 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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77A CYS* 3.7 8.5 - - + +
105A PRO 3.1 16.9 + - - +
106A LEU 3.7 3.4 - - - +
107A PHE 3.3 0.2 - - - -
108A ASN* 1.3 76.3 - - - +
110A CYS* 1.3 57.1 + - - +
112A SER* 2.8 22.7 + - - -
113A GLY* 3.1 9.0 + - - -
114A SER 3.6 5.7 + - - -
117A CYS* 3.9 18.4 - - + -
118A VAL* 3.7 22.4 - - + +
121A LEU* 3.8 16.6 - - + -
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Residues in contact with CYS 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 LEU* 3.2 17.2 + - - +
107A PHE 2.9 12.2 + - - +
109A ALA* 1.3 76.2 - - - +
111A VAL* 1.3 58.7 + - - +
113A GLY 4.0 1.1 - - - +
118A VAL* 3.9 17.3 - - - -
137A PRO* 3.7 31.9 - - + +
140A GLU* 4.6 4.0 - - + -
141A ALA* 4.1 17.9 - - + +
144A ARG* 4.1 4.0 - - - -
146A HIS* 3.0 26.3 + - - -
149A CYS* 4.5 4.7 - - - -
153A LEU* 3.7 22.0 - - - -
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Residues in contact with VAL 111 (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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78A LEU* 4.1 19.5 - - + +
107A PHE* 3.1 31.8 + - + +
108A ASN* 2.9 10.2 + - - +
110A CYS* 1.3 76.6 - - - +
112A SER* 1.3 61.8 + - - +
113A GLY 3.4 0.5 + - - -
140A GLU* 3.6 23.1 - - + +
144A ARG* 3.6 35.3 + - - +
146A HIS* 3.5 12.3 - - - -
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Residues in contact with SER 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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77A CYS 3.3 17.5 + - - -
78A LEU 3.1 25.8 + - - -
79A GLY 4.2 1.6 - - - -
80A GLY* 3.7 11.0 - - - -
108A ASN 2.9 4.6 + - - -
109A ALA* 2.8 17.3 + - - -
111A VAL* 1.3 80.0 - - - +
113A GLY* 1.3 56.8 + - - +
114A SER* 2.9 16.2 + - - -
146A HIS* 4.2 1.9 + - - -
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Residues in contact with GLY 113 (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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109A ALA 3.1 7.5 + - - -
111A VAL 3.3 3.0 - - - -
112A SER* 1.3 79.2 + - - +
114A SER* 1.3 60.1 + - - +
115A TRP* 2.8 10.6 + - - +
146A HIS* 3.5 31.4 + - - -
148A GLU* 3.9 8.1 - - - +
149A CYS* 3.8 9.8 - - - -
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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
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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