Contacts of the helix formed by residues 100 - 110 (chain A) in PDB entry 3G0H
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ARG 3.9 0.8 + - - +
99A LEU* 1.3 79.6 - - - +
101A PRO* 1.3 76.3 - - + +
102A GLN* 3.3 7.6 - - - +
103A LEU* 3.1 26.8 + - + +
104A LEU* 3.0 17.7 + - - +
153A LEU 5.0 0.6 + - - -
154A SER* 3.3 33.3 + - - +
155A GLN 5.6 0.2 - - - -
156A VAL 4.6 11.1 + - - -
189A TYR* 3.7 19.4 + - - +
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Residues in contact with PRO 101 (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 LEU 4.4 1.6 - - - +
100A LYS* 1.3 89.6 - - + +
102A GLN* 1.3 70.4 + - - +
104A LEU* 3.2 10.2 + - + +
105A GLN* 3.0 43.7 + - - +
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Residues in contact with GLN 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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100A LYS* 4.2 1.9 - - - +
101A PRO* 1.3 94.2 - - - +
103A LEU* 1.3 58.6 + - - +
104A LEU 3.3 0.2 - - - -
105A GLN* 3.6 14.5 - - - +
106A GLY* 3.1 20.6 + - - -
185A MET 4.4 2.9 - - - +
186A GLY* 5.7 0.3 - - - -
188A PHE* 3.4 33.8 + - + +
189A TYR* 3.6 41.0 + - + +
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Residues in contact with LEU 103 (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 LEU* 4.2 7.4 - - + +
100A LYS* 3.1 30.9 + - + +
102A GLN* 1.3 77.5 - - - +
104A LEU* 1.3 57.9 + - - +
106A GLY 3.9 1.6 - - - +
107A VAL* 3.1 30.3 + - - +
150A LEU* 3.7 22.3 - - + +
153A LEU* 3.5 37.5 - - + +
154A SER* 3.7 40.8 - - - +
185A MET 4.2 9.1 - - - +
189A TYR* 4.2 20.2 - - + +
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Residues in contact with LEU 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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94A PHE* 3.6 42.8 - - + +
95A GLU* 4.0 29.8 - - + +
99A LEU* 4.5 23.8 - - + +
100A LYS 3.0 10.6 + - - +
101A PRO* 3.6 11.9 - - + +
103A LEU* 1.3 77.4 - - - +
105A GLN* 1.3 59.4 + - + +
106A GLY 3.3 0.2 - - - -
107A VAL* 3.3 3.6 + - + +
108A TYR* 3.0 49.5 + - + -
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Residues in contact with GLN 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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101A PRO* 3.0 26.8 + - - +
102A GLN* 3.6 18.9 - - - +
104A LEU* 1.3 75.1 - - + +
106A GLY* 1.3 54.9 + - - +
108A TYR* 4.1 4.6 - - - +
109A ALA* 2.8 37.1 + - - +
188A PHE* 3.4 31.7 - - + +
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Residues in contact with GLY 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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102A GLN 3.1 10.1 + - - -
103A LEU 4.2 0.9 - - - -
104A LEU 3.3 0.2 - - - -
105A GLN* 1.3 77.5 - - - +
107A VAL* 1.3 62.9 + - - +
109A ALA* 3.6 2.5 + - - +
110A MET* 3.3 25.6 + - - +
184A GLN 4.4 4.2 - - - +
185A MET* 3.6 26.9 - - - -
188A PHE* 3.3 18.3 - - - -
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Residues in contact with VAL 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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94A PHE* 3.7 53.2 - - + -
99A LEU* 4.3 5.4 - - + -
103A LEU 3.1 20.8 + - - +
104A LEU* 3.3 11.2 + - + +
105A GLN 3.2 0.6 - - - -
106A GLY* 1.3 73.2 - - - +
108A TYR* 1.3 71.0 + - + +
110A MET* 3.1 20.8 + - - +
112A PHE* 3.5 22.8 - - + +
150A LEU* 4.0 26.9 - - + -
185A MET* 4.8 4.0 - - - -
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Residues in contact with TYR 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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94A PHE* 3.8 20.2 + + + +
95A GLU* 2.2 44.4 + - - -
104A LEU* 3.0 36.3 + - + +
105A GLN* 4.1 4.7 - - - +
107A VAL* 1.3 79.9 - - + +
109A ALA* 1.3 54.2 + - - +
111A GLY* 2.7 26.7 + - - -
112A PHE 3.3 21.5 - - - -
113A ASN* 4.1 17.0 + - - -
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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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105A GLN 2.8 22.9 + - - +
106A GLY 3.6 5.4 - - - +
107A VAL 3.2 0.2 - - - -
108A TYR* 1.3 73.1 - - - +
110A MET* 1.3 59.8 + - + +
111A GLY 3.2 1.3 + - - -
184A GLN 5.6 0.2 - - - +
187A LYS* 4.9 12.4 + - + +
188A PHE* 3.5 25.8 - - + -
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Residues in contact with MET 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ANP 5.6 1.3 - - - -
106A GLY 3.3 12.1 - - - +
107A VAL* 3.1 11.0 + - - +
109A ALA* 1.3 76.3 - - + +
111A GLY* 1.3 60.4 + - - +
112A PHE* 3.5 34.9 + - + -
181A VAL* 3.5 16.8 - - + +
184A GLN* 3.2 32.1 - - + +
185A MET* 3.0 49.6 - - + +
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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