Contacts of the helix formed by residues 80 - 100 (chain A) in PDB entry 2V3V
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 SER 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A PRO* 4.0 0.7 - - - -
79A VAL* 1.3 81.1 - - - +
81A TRP* 1.3 58.7 + - - +
82A ASP* 3.6 8.7 + - - +
83A GLU* 3.0 27.5 + - - +
84A ALA* 2.9 28.6 + - - +
490A GLN* 5.5 2.7 - - - +
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Residues in contact with TRP 81 (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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66A PRO* 3.6 15.5 - - + +
80A SER* 1.3 73.5 - - - +
82A ASP* 1.3 57.5 + - - +
84A ALA* 3.4 2.3 + - + +
85A LEU* 2.9 60.9 + - + +
459A LEU* 3.9 33.2 - - + -
460A PRO* 3.4 35.5 - - + +
490A GLN* 2.6 56.0 + - + +
492A ARG* 3.4 50.1 - - + +
497A THR* 3.5 34.3 - - + -
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.2 8.6 + - - +
81A TRP* 1.3 79.9 - - - +
83A GLU* 1.3 60.0 + - - +
85A LEU* 5.3 0.7 - - - -
86A ASP* 3.2 30.8 + - - +
504A ARG* 3.1 36.3 + - - +
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Residues in contact with GLU 83 (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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70A ARG* 2.7 36.0 + - - -
79A VAL* 3.4 23.2 - - + +
80A SER* 3.0 21.5 + - - +
82A ASP* 1.3 72.3 - - - +
84A ALA* 1.3 65.5 + - - +
86A ASP* 3.4 5.7 + - - +
87A LEU* 3.0 34.8 + - + +
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Residues in contact with ALA 84 (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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66A PRO* 3.9 20.4 - - + -
79A VAL* 4.0 4.7 - - + +
80A SER 2.9 18.5 + - - +
81A TRP* 3.6 6.7 - - + +
83A GLU* 1.3 77.3 - - - +
85A LEU* 1.3 57.4 + - - +
87A LEU* 3.4 3.6 - - - +
88A MET* 2.9 30.1 + - - +
457A LEU* 3.8 20.9 - - + +
459A LEU* 4.0 19.7 - - + -
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Residues in contact with LEU 85 (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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81A TRP* 2.9 51.3 + - + +
82A ASP* 5.3 0.2 - - - -
84A ALA* 1.3 78.9 - - - +
86A ASP* 1.3 57.8 + - - +
88A MET* 3.4 11.8 + - - +
89A ALA* 2.9 31.7 + - - +
459A LEU* 5.0 1.6 - - + -
492A ARG* 4.4 11.4 - - - +
497A THR* 4.2 12.8 - - + +
500A GLU* 3.8 23.3 - - + -
501A PHE* 4.2 33.3 - - + +
504A ARG* 3.6 23.2 + - - +
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Residues in contact with ASP 86 (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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82A ASP* 3.2 24.6 + - - +
83A GLU* 3.9 5.0 - - - +
85A LEU* 1.3 70.9 - - - +
87A LEU* 1.3 58.7 + - - +
89A ALA* 4.1 4.0 - - - +
90A SER* 2.8 38.4 + - - -
504A ARG* 3.1 28.3 + - - +
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Residues in contact with LEU 87 (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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68A VAL* 4.0 27.4 - - + -
70A ARG* 4.3 13.2 - - - +
79A VAL* 5.4 1.1 - - + -
83A GLU* 3.0 30.2 + - + +
84A ALA* 3.4 5.2 - - - +
86A ASP* 1.3 74.9 - - - +
88A MET* 1.3 60.1 + - - +
90A SER* 3.3 5.2 + - - +
91A ARG* 3.1 44.4 + - + +
439A PHE* 4.6 11.7 - - + -
457A LEU* 4.7 8.5 - - + -
817A LCP 3.3 23.6 - - - +
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Residues in contact with MET 88 (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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84A ALA 2.9 16.9 + - - +
85A LEU* 3.6 10.5 - - - +
87A LEU* 1.3 77.1 - - - +
89A ALA* 1.3 60.4 + - - +
91A ARG* 3.9 0.5 - - - +
92A PHE* 3.2 33.8 + - + -
413A ILE* 3.4 40.2 - - + -
439A PHE* 4.1 9.8 - - - -
441A VAL* 3.9 26.2 - - + -
443A ILE* 5.6 0.7 - - + -
457A LEU* 4.0 5.8 - - + +
459A LEU* 3.8 26.9 - - + -
497A THR* 5.7 1.1 - - + -
498A LEU* 5.5 4.3 - - + -
501A PHE* 3.6 34.5 - - + -
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Residues in contact with ALA 89 (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 2.9 18.1 + - - +
86A ASP* 4.1 3.8 - - - +
88A MET* 1.3 73.8 - - - +
90A SER* 1.3 61.2 + - - +
93A ARG* 3.0 31.7 + - - +
501A PHE* 4.0 9.9 - - + +
504A ARG* 3.6 19.1 - - + +
505A ALA* 3.5 37.4 - - + +
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Residues in contact with SER 90 (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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86A ASP 2.8 22.5 + - - -
87A LEU* 3.3 10.6 + - - +
89A ALA* 1.3 74.7 - - - +
91A ARG* 1.3 64.4 + - - +
93A ARG* 4.0 4.0 - - - +
94A SER* 2.9 34.2 + - - -
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Residues in contact with ARG 91 (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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87A LEU* 3.1 27.7 + - + +
88A MET 3.9 0.4 - - - +
90A SER* 1.3 83.3 + - - +
92A PHE* 1.3 57.0 + - - +
94A SER* 3.6 5.6 + - - -
95A SER* 3.1 30.5 + - - -
411A CYS* 3.7 5.8 - - - -
437A GLU 5.0 5.9 + - - -
438A SER 4.9 3.4 + - - -
439A PHE* 3.7 52.8 - - + +
817A LCP 2.8 53.6 + - - +
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Residues in contact with PHE 92 (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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88A MET* 3.2 28.3 + - + +
89A ALA 4.2 1.6 - - - +
91A ARG* 1.3 75.7 - - - +
93A ARG* 1.3 65.5 + - - +
95A SER* 3.5 2.1 + - - -
96A ILE* 3.2 30.7 + - - +
104A VAL* 3.7 32.3 - - + +
105A ALA 4.3 0.9 - - - -
124A PHE* 3.9 18.2 - + - -
128A PHE* 4.3 13.7 - + + -
411A CYS* 3.7 28.0 - - + -
412A MET 3.8 11.0 - - - -
413A ILE* 3.5 28.0 - - + -
439A PHE* 4.1 17.3 - + - -
441A VAL* 4.3 7.9 - - + -
501A PHE* 3.9 26.2 - + + -
505A ALA* 5.1 0.4 - - + -
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Residues in contact with ARG 93 (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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89A ALA 3.0 20.4 + - - +
90A SER* 4.0 4.9 - - - +
92A PHE* 1.3 78.4 - - - +
94A SER* 1.3 57.4 + - - +
96A ILE* 3.4 35.2 + - - +
97A ASP* 2.9 52.9 + - - +
128A PHE* 4.1 20.0 + - - +
504A ARG 5.6 0.7 - - - +
505A ALA* 2.8 41.7 + - - +
506A GLY* 4.3 14.1 + - - -
507A VAL* 4.7 0.6 - - - +
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Residues in contact with SER 94 (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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90A SER 2.9 22.7 + - - -
91A ARG* 3.6 7.1 + - - -
93A ARG* 1.3 75.1 - - - +
95A SER* 1.3 61.5 + - - +
97A ASP* 3.4 14.9 - - - +
98A MET* 3.0 36.4 + - - +
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Residues in contact with SER 95 (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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91A ARG 3.1 20.2 + - - -
92A PHE 3.8 4.5 - - - -
93A ARG 3.2 0.2 - - - -
94A SER* 1.3 75.6 + - - +
96A ILE* 1.3 55.6 + - - +
99A TYR* 2.8 45.5 + - - -
103A SER* 2.8 34.4 + - - -
104A VAL* 4.0 3.2 - - - +
410A LYS* 4.0 6.7 - - - +
411A CYS* 3.7 21.0 - - - -
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Residues in contact with ILE 96 (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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92A PHE 3.2 17.6 + - - +
93A ARG* 3.4 30.5 - - - +
95A SER* 1.3 74.4 - - - +
97A ASP* 1.3 63.3 + - - +
100A GLY* 2.9 27.8 + - - -
101A PRO* 3.9 30.5 - - + -
104A VAL* 3.9 16.8 - - + -
128A PHE* 3.5 51.8 - - + +
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Residues in contact with ASP 97 (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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93A ARG* 2.9 49.0 + - - +
94A SER* 3.4 19.2 - - - +
96A ILE* 1.3 78.2 - - - +
98A MET* 1.3 61.7 + - + +
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Residues in contact with MET 98 (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 SER* 3.0 22.8 + - - +
97A ASP* 1.3 82.3 - - + +
99A TYR* 1.3 102.3 + - + +
100A GLY 3.8 0.4 - - - -
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Residues in contact with TYR 99 (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 SER* 2.8 35.0 + - - +
98A MET* 1.3 113.1 - - + +
100A GLY* 1.3 61.9 + - - +
102A ASN* 5.1 1.0 + - - +
103A SER* 3.8 15.8 + - - -
410A LYS* 3.6 42.0 - - + +
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Residues in contact with GLY 100 (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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96A ILE* 2.9 22.4 + - - -
97A ASP 5.0 0.2 + - - -
98A MET 3.8 0.4 - - - -
99A TYR* 1.3 76.9 - - - +
101A PRO* 1.3 66.6 - - - +
102A ASN 3.1 8.3 + - - -
103A SER* 2.7 29.1 + - - -
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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