Contacts of the helix formed by residues 89 - 103 (chain E) in PDB entry 4V1M
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 GLY 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E GLU* 4.6 0.4 + - - -
87E SER 3.9 3.4 + - - -
88E VAL* 1.3 75.3 - - - +
90E VAL* 1.4 53.7 + - - -
91E LYS* 2.8 19.3 + - - -
92E THR* 2.9 20.9 + - - -
93E MET* 3.2 8.3 + - - +
117E THR* 3.4 15.3 - - - -
120E ALA* 3.7 5.8 - - - -
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Residues in contact with VAL 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E GLY* 1.4 67.2 - - - -
91E LYS* 1.3 65.6 + - + +
92E THR 3.6 0.2 - - - -
93E MET* 4.0 2.7 - - - -
94E LYS* 3.1 30.2 + - + +
117E THR* 3.8 2.0 + - - -
119E SER* 4.0 31.9 - - - +
120E ALA* 3.5 14.4 - - - +
123E LEU* 3.7 24.5 - - + -
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Residues in contact with LYS 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E GLY* 2.8 7.2 + - - +
90E VAL* 1.3 82.9 - - + +
92E THR* 1.3 61.0 + - - +
94E LYS* 3.9 3.4 + - - +
95E THR* 3.1 21.3 + - - -
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Residues in contact with THR 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E GLU* 4.7 5.5 - - - +
83E CYS* 3.9 16.2 - - - -
85E GLU* 2.6 42.5 + - - +
88E VAL* 4.1 10.3 - - + -
89E GLY 2.9 11.8 + - - -
91E LYS* 1.3 74.1 - - - +
93E MET* 1.3 63.4 + - - +
95E THR* 3.4 20.8 - - + +
96E PHE* 3.5 10.6 + - - +
110E PHE* 4.9 5.8 - - + -
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Residues in contact with MET 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E VAL* 4.8 7.1 - - + +
89E GLY 3.2 7.0 + - - +
90E VAL 4.1 0.9 - - - +
92E THR* 1.3 73.4 - - - +
94E LYS* 1.4 55.3 + - - +
95E THR 3.1 2.1 + - - -
96E PHE* 3.2 32.3 + - - +
97E VAL* 2.8 50.9 + - + +
110E PHE* 4.6 13.5 - - + -
116E ILE* 3.8 42.4 - - + -
120E ALA* 3.5 38.1 - - + +
123E LEU* 3.8 8.1 - - + -
124E VAL* 4.9 14.4 - - + -
132E ILE* 5.3 1.3 - - + -
134E THR* 5.0 2.5 - - + -
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Residues in contact with LYS 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E VAL* 3.1 22.9 + - + +
91E LYS* 4.3 4.0 - - - +
92E THR 3.6 0.2 - - - -
93E MET* 1.4 73.5 - - - +
95E THR* 1.4 60.8 + - - +
97E VAL* 4.4 8.1 - - + -
98E ILE* 3.3 53.0 + - + +
123E LEU* 3.9 24.3 - - + +
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Residues in contact with THR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E GLU* 5.8 4.3 - - - +
91E LYS 3.1 16.1 + - - -
92E THR* 3.4 15.3 - - + +
94E LYS* 1.4 77.4 - - - +
96E PHE* 1.3 60.7 + - - +
98E ILE* 4.2 1.7 - - - +
99E HIS* 3.2 23.8 + - + +
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Residues in contact with PHE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E TRP* 3.6 20.6 - + - -
81E GLU* 3.3 40.4 - - + +
92E THR 3.5 6.3 + - - +
93E MET* 3.2 25.7 + - - +
95E THR* 1.3 75.5 - - - +
97E VAL* 1.4 68.4 + - + +
99E HIS* 3.2 20.5 + - - +
100E ILE* 3.3 39.6 + - + +
108E GLY 4.0 20.2 - - - -
109E ILE 3.9 5.6 - - - -
110E PHE* 3.7 27.8 - + + -
132E ILE* 3.7 25.4 - - + -
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Residues in contact with VAL 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E MET* 2.8 49.7 + - + +
94E LYS* 4.0 11.2 - - + +
96E PHE* 1.4 76.0 - - + +
98E ILE* 1.3 65.0 + - + +
100E ILE* 3.4 5.6 + - - +
101E GLN 3.5 0.2 + - - -
123E LEU* 3.9 20.0 - - + +
126E SER* 3.8 15.9 - - - +
127E ILE* 3.4 47.4 - - + +
132E ILE* 4.0 14.4 - - + -
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Residues in contact with ILE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 3.3 53.3 + - + +
95E THR* 4.5 2.2 - - - +
97E VAL* 1.3 75.2 - - + +
99E HIS* 1.4 59.2 + - - +
101E GLN* 3.1 19.0 + - - +
102E GLU* 2.9 58.6 + - + +
127E ILE* 6.0 0.7 - - + -
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Residues in contact with HIS 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E TRP* 3.5 52.4 - + - -
81E GLU* 4.3 7.2 - - - -
95E THR* 3.2 17.7 + - + +
96E PHE* 3.2 15.3 - - - +
97E VAL 3.3 0.2 - - - -
98E ILE* 1.4 74.9 - - - +
100E ILE* 1.3 54.2 + - - +
102E GLU* 4.1 6.5 - - - +
103E LYS* 3.1 55.1 + - + +
105E PHE* 4.0 10.1 - + - -
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Residues in contact with ILE 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E TRP* 3.9 13.5 - - + -
96E PHE* 3.3 56.7 + - + +
97E VAL* 3.8 7.0 - - - +
98E ILE 3.2 0.4 - - - -
99E HIS* 1.3 76.8 - - - +
101E GLN* 1.4 61.1 + - - +
103E LYS 3.8 0.2 + - - -
104E ASN* 3.2 3.5 + - - -
105E PHE* 2.9 62.1 + - + +
107E THR 5.2 5.4 - - - +
108E GLY* 4.2 10.8 - - - -
127E ILE* 3.7 17.9 - - + -
130E ALA* 3.9 16.2 - - + -
131E THR 5.4 0.4 - - - +
132E ILE* 5.2 7.6 - - + -
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E VAL 3.5 4.6 + - - +
98E ILE* 3.1 22.4 + - - +
100E ILE* 1.4 78.2 - - - +
102E GLU* 1.3 63.3 + - + +
104E ASN* 3.7 17.6 + - - +
127E ILE* 3.5 46.5 - - + +
128E PRO 5.4 3.0 + - - +
130E ALA* 5.8 2.0 - - - -
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Residues in contact with GLU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ILE* 2.9 41.2 + - + +
99E HIS* 4.2 6.1 - - - +
101E GLN* 1.3 74.6 - - + +
103E LYS* 1.4 58.8 + - + +
104E ASN* 3.1 13.5 + - - +
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Residues in contact with LYS 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E GLN* 6.3 0.2 - - - +
99E HIS* 3.1 44.6 + - + +
101E GLN 3.6 0.2 - - - -
102E GLU* 1.4 73.4 - - + +
104E ASN* 1.4 63.9 + - - +
105E PHE* 3.2 32.6 + - + -
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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