Contacts of the helix formed by residues 64 - 78 (chain A) in PDB entry 3VAS
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN 3.3 22.4 - - - -
16A LEU* 4.0 5.2 + - - +
63A GLY* 1.3 71.6 - - - -
65A ALA* 1.3 57.2 + - - -
66A THR 3.4 2.5 - - - -
67A LEU* 3.2 4.6 + - - -
68A ASN* 2.8 38.3 + - - +
401A ADN 3.1 22.4 + - - -
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Residues in contact with ALA 65 (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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64A GLY* 1.3 71.4 - - - +
66A THR* 1.3 62.4 + - - +
68A ASN* 3.4 3.1 + - - +
69A THR* 3.2 25.9 + - - -
165A TYR* 4.9 1.6 - - - +
167A ALA* 4.2 10.1 - - + -
169A PHE* 3.5 37.0 - - + -
197A SER* 5.3 0.2 - - - +
302A ASP* 3.7 27.2 - - - +
401A ADN 3.2 16.1 + - - +
402A CL 4.3 0.4 - - + -
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Residues in contact with THR 66 (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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12A MET 3.4 32.2 + - - +
13A GLY* 4.1 3.8 - - - -
65A ALA* 1.3 77.3 - - - +
67A LEU* 1.3 58.0 + - - +
69A THR* 3.3 2.6 + - - -
70A VAL* 3.0 32.8 + - + +
85A TYR* 4.1 5.8 - - + -
165A TYR* 3.4 34.8 - - + +
167A ALA* 3.1 21.7 + - - +
170A VAL* 4.0 0.7 - - - +
402A CL 3.0 21.9 - - - +
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Residues in contact with LEU 67 (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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15A PRO* 4.3 10.8 - - + -
62A ALA* 5.4 2.2 - - + -
63A GLY 3.8 17.3 - - - +
64A GLY* 3.2 9.4 + - - +
66A THR* 1.3 76.2 - - - +
68A ASN* 1.3 65.7 + - - +
70A VAL 4.6 0.2 - - - +
71A LYS* 3.0 43.3 + - + +
85A TYR* 3.7 36.9 + - + +
98A ILE* 3.9 27.4 - - + -
102A CYS* 3.8 16.2 - - - -
107A LEU* 3.6 29.2 - - + -
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Residues in contact with ASN 68 (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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62A ALA 4.0 2.6 - - - +
63A GLY* 3.7 14.6 - - - +
64A GLY 2.8 23.5 + - - +
65A ALA 3.5 5.2 - - - +
66A THR 3.3 0.2 - - - -
67A LEU* 1.3 72.2 - - - +
69A THR* 1.3 61.9 + - - +
71A LYS* 3.6 7.9 - - - +
72A MET* 3.2 17.8 + - - +
299A GLY* 4.9 0.4 - - - -
302A ASP* 3.1 22.3 + - + -
338A PHE* 3.2 62.5 - - + +
401A ADN 3.2 24.9 + - - -
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Residues in contact with THR 69 (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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65A ALA 3.2 7.4 + - - -
66A THR 3.7 1.6 - - - -
68A ASN* 1.3 78.8 - - - +
70A VAL* 1.3 59.0 + - - +
72A MET 3.3 1.0 + - - -
73A ILE* 3.0 39.5 + - + +
165A TYR* 3.4 51.1 + - + -
302A ASP* 2.8 31.5 + - - -
305A ALA* 4.0 1.3 - - + -
306A ALA* 3.3 26.1 - - - +
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Residues in contact with VAL 70 (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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9A VAL* 4.9 6.3 - - + -
10A PHE 4.8 0.9 - - - -
11A GLY* 3.9 24.0 - - - +
66A THR* 3.0 26.0 + - + +
67A LEU* 4.2 2.5 - - - +
69A THR* 1.3 76.4 - - + +
71A LYS* 1.3 63.3 + - - +
73A ILE* 3.3 9.2 + - + +
74A GLN* 3.1 20.6 + - - +
83A CYS* 3.7 13.4 - - + -
84A SER 3.8 12.6 - - - +
85A TYR* 4.6 6.3 - - + -
107A LEU* 3.7 25.6 - - + -
165A TYR* 4.3 17.0 - - + -
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Residues in contact with LYS 71 (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 ILE* 6.1 0.4 - - - +
62A ALA* 3.9 24.7 + - - +
63A GLY 5.6 0.2 + - - -
67A LEU* 3.0 36.9 + - + +
68A ASN* 3.6 12.2 + - - +
70A VAL* 1.3 77.8 - - - +
72A MET* 1.3 60.5 + - - +
74A GLN* 3.4 7.8 + - - +
75A TRP* 2.9 26.5 + - - +
101A ASP* 3.0 25.4 + - - +
102A CYS* 5.5 2.9 - - - -
105A LEU* 3.7 27.1 - - + +
107A LEU* 3.7 23.3 - - + -
338A PHE* 4.0 29.2 + - - -
340A LEU* 4.1 8.8 - - + +
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Residues in contact with MET 72 (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 ASN 3.2 19.6 + - - +
71A LYS* 1.3 76.9 - - - +
73A ILE* 1.3 56.6 + - - +
75A TRP* 4.0 13.9 - - + -
76A ILE* 2.7 46.9 + - + +
303A ALA* 3.7 26.7 - - - -
306A ALA* 3.7 13.9 - - + -
328A ALA* 3.7 36.1 - - + +
331A TYR* 4.2 9.0 - - + -
332A ILE* 4.3 1.3 - - + -
338A PHE* 3.8 16.4 - - + -
340A LEU* 3.9 28.3 - - + -
346A TYR* 4.1 7.6 - - - +
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Residues in contact with ILE 73 (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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9A VAL* 4.3 23.8 - - + -
69A THR* 3.0 33.8 + - + +
70A VAL* 3.5 11.9 - - + +
72A MET* 1.3 75.3 - - - +
74A GLN* 1.3 58.9 + - - +
76A ILE* 3.4 0.7 + - - +
77A ILE* 3.0 49.1 + - + +
83A CYS* 3.7 15.5 - - - -
165A TYR* 5.1 2.9 - - + -
306A ALA* 3.7 20.4 - - - +
309A ILE* 3.9 28.3 - - + -
310A ALA* 4.3 13.2 - - + -
313A ILE* 5.0 1.1 - - + -
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Residues in contact with GLN 74 (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 VAL 3.1 13.2 + - - +
71A LYS* 3.4 12.1 - - - +
73A ILE* 1.3 78.1 - - - +
75A TRP* 1.3 56.7 + - - +
77A ILE* 3.9 0.5 - - - +
78A GLN* 2.9 26.8 + - - +
79A LYS 2.6 32.9 + - - +
80A PRO* 3.7 3.2 - - - +
81A PHE 3.6 4.8 - - - +
82A VAL* 3.1 9.4 + - - +
83A CYS* 2.9 42.4 + - + +
105A LEU* 3.2 24.2 + - + +
106A ASP* 3.5 17.1 + - - +
107A LEU* 4.2 6.1 - - + +
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Residues in contact with TRP 75 (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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71A LYS 2.9 16.6 + - - +
72A MET* 3.1 13.4 + - + +
74A GLN* 1.3 76.7 - - - +
76A ILE* 1.3 83.0 + - + +
78A GLN* 3.5 9.8 + - - +
105A LEU* 3.9 27.6 - - + -
331A TYR* 3.7 23.1 - + - -
340A LEU* 3.8 28.8 - - + +
341A GLY 3.0 29.4 + - - -
342A SER 4.0 1.8 - - - -
343A ARG* 3.0 51.4 + - + +
346A TYR* 3.5 51.6 - + + -
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Residues in contact with ILE 76 (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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72A MET* 2.7 37.3 + - + +
73A ILE 3.8 3.4 - - - +
75A TRP* 1.3 88.1 - - + +
77A ILE* 1.3 62.7 + - - +
78A GLN* 3.4 1.9 + - - +
306A ALA 4.2 5.4 - - - +
307A GLY* 3.9 30.3 - - - +
310A ALA* 3.8 16.6 - - + -
311A ASP* 5.0 2.5 - - - +
314A ARG* 3.9 17.5 + - - +
343A ARG* 2.8 34.8 + - - +
346A TYR* 4.0 25.4 - - + +
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Residues in contact with ILE 77 (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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4A LEU* 3.7 34.5 - - + +
9A VAL* 5.4 0.2 - - + -
73A ILE* 3.0 35.6 + - + +
74A GLN 4.3 1.8 - - - +
76A ILE* 1.3 72.7 - - - +
78A GLN* 1.3 66.0 + - - +
79A LYS* 3.0 21.7 + - + +
82A VAL* 4.3 20.0 - - + -
310A ALA* 4.0 23.6 - - + +
313A ILE* 4.2 5.2 - - + -
314A ARG* 4.1 26.9 + - - +
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Residues in contact with GLN 78 (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 GLN* 2.9 17.5 + - - +
75A TRP* 3.8 4.9 - - - +
76A ILE 3.2 6.2 - - - +
77A ILE* 1.3 77.7 - - - +
79A LYS* 1.3 58.7 + - - +
80A PRO* 3.9 6.1 - - - +
343A ARG* 3.6 44.6 + - + +
344A ASP* 5.0 7.9 + - - -
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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
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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