Contacts of the helix formed by residues 59 - 73 (chain A) in PDB entry 1V1A
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 ASP 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLY 3.3 3.8 + - - +
58A GLU* 1.3 75.4 - - - +
60A GLU* 1.3 64.9 + - - +
61A LEU* 4.3 4.9 - - - -
62A GLY* 2.9 15.1 + - - -
63A ALA 3.2 8.7 + - - -
81A ARG* 2.6 25.4 + - - +
84A GLY 4.9 1.1 - - - +
85A PHE* 3.2 14.3 - - - +
86A THR* 2.7 46.0 + - - -
100B ARG* 4.2 10.1 - - - +
102B PHE* 3.7 23.0 - - + +
104B TYR* 4.2 5.1 + - - -
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Residues in contact with GLU 60 (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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59A ASP* 1.3 76.1 - - - +
61A LEU* 1.3 66.6 + - + +
63A ALA* 3.3 6.9 + - - +
64A MET* 3.1 15.2 + - - +
21B HIS* 3.0 21.2 - - - -
22B LEU* 3.6 20.6 - - + -
23B ARG* 2.6 67.1 + - - +
92B GLU* 3.2 23.6 - - - +
100B ARG* 4.7 5.9 + - - +
102B PHE* 3.6 23.0 - - + -
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Residues in contact with LEU 61 (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 VAL* 3.8 36.2 - - + +
14A LEU* 6.3 0.4 - - + -
30A VAL* 4.9 4.3 - - + -
59A ASP* 3.7 4.0 + - - +
60A GLU* 1.3 75.9 - - + +
62A GLY* 1.3 60.1 + - - +
64A MET* 2.8 41.1 + - + +
65A VAL* 2.8 19.3 + - - +
86A THR* 4.0 10.3 - - - +
88A LEU* 4.2 12.3 - - + -
22B LEU* 4.7 13.5 - - + +
28B LEU* 6.2 1.1 - - + -
90B LEU* 3.7 32.8 - - + -
102B PHE* 6.0 1.3 - - + -
104B TYR* 3.9 19.1 - - + +
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Residues in contact with GLY 62 (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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56A VAL* 3.5 26.2 - - - +
57A GLY 4.1 2.0 - - - -
59A ASP* 2.9 14.2 + - - -
61A LEU* 1.3 74.9 - - - +
63A ALA* 1.3 56.2 + - - +
65A VAL* 3.1 4.3 + - - +
66A GLU* 2.8 29.5 + - - +
81A ARG* 4.4 1.6 - - - -
86A THR* 3.0 22.4 + - - -
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Residues in contact with ALA 63 (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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59A ASP 3.2 7.2 + - - +
60A GLU 3.3 10.5 - - - +
61A LEU 3.1 0.2 - - - -
62A GLY* 1.3 77.3 - - - +
64A MET* 1.3 51.0 + - - +
66A GLU* 3.4 8.0 + - - +
67A GLU* 2.7 42.1 + - + +
81A ARG* 3.3 31.7 - - - +
23B ARG* 3.7 28.5 - - - +
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Residues in contact with MET 64 (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 VAL* 5.0 5.4 - - - -
30A VAL* 3.9 28.0 - - + +
31A TYR 5.6 0.7 - - - +
32A VAL* 3.8 16.4 - - + +
60A GLU 3.1 10.8 + - - +
61A LEU* 2.8 24.8 + - + +
63A ALA* 1.3 75.6 - - - +
65A VAL* 1.3 60.8 + - + +
67A GLU* 4.0 5.8 - - + +
68A ARG* 3.1 24.3 + - - +
22B LEU 3.2 20.6 - - - +
23B ARG* 2.9 34.7 - - - +
25B LYS* 3.3 17.7 - - + +
26B ARG* 5.8 0.2 - - + -
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Residues in contact with VAL 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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10A PRO* 3.7 20.4 - - + -
11A LEU 4.7 7.2 - - - +
12A VAL* 4.2 14.4 - - + -
32A VAL* 4.3 17.9 - - + +
37A VAL* 5.3 2.0 - - + -
56A VAL* 3.6 17.5 - - + -
61A LEU 2.8 16.6 + - - +
62A GLY 3.1 6.9 + - - +
64A MET* 1.3 74.7 - - - +
66A GLU* 1.3 64.8 + - - +
68A ARG* 3.2 3.6 + - - +
69A LEU* 3.0 44.6 + - + +
79A PHE* 4.0 0.2 - - + -
86A THR* 4.0 22.2 - - + -
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Residues in contact with GLU 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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62A GLY 2.8 14.8 + - - +
63A ALA* 3.5 5.3 - - - +
65A VAL* 1.3 78.6 - - - +
67A GLU* 1.3 58.6 + - + +
69A LEU* 3.4 4.1 + - - +
70A ARG* 2.5 60.0 + - - +
76A LEU* 3.9 2.7 - - + +
79A PHE* 3.7 27.4 - - + -
80A ARG* 6.0 2.0 - - - -
81A ARG* 2.9 38.5 + - - +
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Residues in contact with GLU 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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63A ALA* 2.7 28.2 + - + +
64A MET* 4.1 5.8 - - - +
66A GLU* 1.3 73.6 - - + +
68A ARG* 1.3 61.2 + - - +
70A ARG* 3.6 8.9 + - - +
71A ALA* 2.9 27.9 + - - +
23B ARG* 3.6 35.9 + - - +
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Residues in contact with ARG 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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32A VAL* 3.7 32.3 - - + +
41A VAL* 5.0 3.4 - - + -
45A ARG* 4.4 5.9 - - - +
64A MET 3.1 17.8 + - - +
65A VAL 3.7 3.6 - - - +
67A GLU* 1.3 73.8 - - - +
69A LEU* 1.3 69.0 + - + +
71A ALA* 3.1 15.6 + - - +
72A GLU* 2.7 61.8 + - + +
288A HIS* 4.3 14.8 + - + +
289A GLU* 5.2 12.6 + - - +
26B ARG* 5.4 8.5 - - - +
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Residues in contact with LEU 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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32A VAL* 5.7 0.4 - - + -
37A VAL* 4.0 28.9 - - + +
40A ALA* 5.7 0.2 - - + -
41A VAL* 5.1 2.9 - - + -
52A PHE* 4.5 11.2 - - + -
65A VAL* 3.0 27.6 + - + +
66A GLU 3.5 4.9 - - - +
68A ARG* 1.3 78.7 - - + +
70A ARG* 1.3 61.6 + - - +
72A GLU* 3.2 4.6 + - - +
73A GLY 3.0 18.7 + - - -
74A VAL* 3.2 36.5 + - + -
76A LEU* 3.2 33.4 - - + -
79A PHE* 3.6 30.1 - - + -
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Residues in contact with ARG 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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66A GLU* 2.5 59.3 + - - +
67A GLU* 3.9 8.7 - - - +
69A LEU* 1.3 76.5 - - - +
71A ALA* 1.3 66.1 + - - +
72A GLU 3.2 0.9 + - - -
73A GLY* 3.2 12.8 + - - -
74A VAL 5.0 3.4 - - - -
76A LEU* 4.0 19.8 - - - +
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Residues in contact with ALA 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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67A GLU 2.9 19.7 + - - +
68A ARG* 3.1 25.3 + - - +
70A ARG* 1.3 79.1 - - - +
72A GLU* 1.3 62.8 + - - +
73A GLY* 4.7 0.2 - - - -
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Residues in contact with GLU 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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41A VAL* 3.4 31.4 - - + -
44A ALA* 4.1 23.3 - - + +
45A ARG* 3.2 38.5 + - - +
68A ARG* 2.7 52.1 + - - +
69A LEU 3.7 5.8 - - - +
70A ARG 3.1 0.2 - - - -
71A ALA* 1.3 79.4 - - - +
73A GLY* 1.3 58.1 + - - +
74A VAL* 4.3 5.6 - - + -
293A TYR* 4.7 6.7 + - - -
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Residues in contact with GLY 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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44A ALA* 4.6 5.7 - - - +
50A VAL* 4.4 3.5 + - - +
69A LEU 3.0 3.8 + - - -
70A ARG* 3.2 10.7 + - - -
72A GLU* 1.3 79.3 - - - +
74A VAL* 1.3 66.3 + - - +
75A ASP* 3.5 3.3 + - - -
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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