Contacts of the helix formed by residues 68 - 83 (chain A) in PDB entry 1QVA
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLN 3.6 0.8 + - - -
67A SER* 1.3 76.9 - - - +
69A THR* 1.3 65.3 + - - -
70A GLY 3.0 5.1 + - - -
71A LYS* 3.3 5.0 + - - +
72A THR* 3.1 29.0 + - - -
104A GLN* 5.5 8.4 - - - +
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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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39A TYR* 4.7 13.0 + - - -
41A PHE* 3.2 39.1 - - + -
48A GLN* 3.5 0.3 - - - +
68A GLY* 1.3 70.6 - - - -
70A GLY* 1.3 63.6 + - - +
72A THR* 5.0 2.5 - - - -
73A GLY 3.3 15.3 + - - +
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Residues in contact with GLY 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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45A SER* 3.7 20.0 - - - -
47A ILE* 5.0 2.9 - - - -
48A GLN* 3.1 15.1 - - - +
68A GLY* 3.0 1.6 + - - -
69A THR* 1.3 80.3 - - - +
71A LYS* 1.3 65.4 + - - +
74A THR* 3.0 27.0 + - - -
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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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47A ILE* 4.8 3.9 - - + +
65A ALA* 3.5 40.3 + - + +
66A GLN 3.4 13.4 + - - +
67A SER* 2.9 38.4 + - - +
68A GLY 3.3 3.2 + - - +
70A GLY* 1.3 73.6 - - - +
72A THR* 1.3 77.6 + - - +
74A THR* 2.9 26.1 + - - -
75A PHE* 3.4 8.7 + - + -
169A ASP* 3.0 32.0 + - - +
170A GLU* 3.4 14.3 - - + +
199A LEU* 4.1 24.9 - - + -
200A SER* 6.0 0.2 - - - -
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Residues in contact with THR 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 GLY 3.1 18.4 + - - -
69A THR* 4.8 2.9 - - - -
71A LYS* 1.3 87.5 - - - +
73A GLY* 1.3 56.2 + - - +
75A PHE* 3.5 22.6 + - + -
76A SER* 2.7 48.2 + - - +
104A GLN* 4.5 12.4 + - - +
105A ILE* 4.4 15.6 - - + +
108A VAL* 4.0 29.2 - - + -
169A ASP* 5.0 1.9 + - - -
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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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41A PHE* 4.1 13.7 - - - -
48A GLN* 4.0 5.6 - - - -
69A THR 3.3 18.5 + - - -
70A GLY 3.8 0.4 - - - -
71A LYS 3.1 0.8 - - - -
72A THR* 1.3 79.8 - - - +
74A THR* 1.3 56.0 + - - +
76A SER* 4.4 4.0 - - - -
77A ILE* 2.7 46.5 + - - +
108A VAL* 5.1 3.8 - - - +
112A LEU* 6.0 0.4 - - - -
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Residues in contact with THR 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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47A ILE* 3.2 21.1 - - + +
48A GLN* 3.2 11.9 + - - +
51A ALA* 3.5 32.5 - - + -
52A ILE* 4.0 15.2 - - - +
55A ILE* 3.8 15.5 - - + -
70A GLY 3.0 18.9 + - - -
71A LYS* 2.9 13.1 + - - -
73A GLY* 1.3 78.8 - - - +
75A PHE* 1.3 61.2 + - + +
78A ALA* 3.1 24.6 + - - +
199A LEU* 5.3 8.3 - - + -
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Residues in contact with PHE 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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55A ILE* 4.4 10.3 - - + -
71A LYS 3.4 15.1 + - - -
72A THR* 3.6 24.7 - - + -
74A THR* 1.3 80.4 - - + +
76A SER* 1.3 76.1 + - - +
78A ALA* 3.9 5.5 - - - +
79A ALA* 2.9 32.1 + - - +
94A MET* 3.8 25.1 - - + -
105A ILE* 3.8 28.5 - - + -
165A MET* 4.9 0.2 - - - +
167A ILE* 3.9 29.0 - - + +
169A ASP* 3.5 30.1 - - + -
197A VAL* 5.0 0.9 - - + -
199A LEU* 3.8 21.3 - - + -
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Residues in contact with SER 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 THR* 2.7 37.7 + - - +
73A GLY* 4.0 3.6 - - - -
75A PHE* 1.3 85.3 - - - +
77A ILE* 1.3 65.6 + - - +
79A ALA* 3.8 1.0 - - - +
80A LEU* 3.1 32.0 + - - +
94A MET* 4.4 2.9 - - - +
108A VAL* 4.2 9.3 - - - +
109A VAL* 3.3 35.8 - - - +
112A LEU* 5.2 3.4 - - - -
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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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23A PHE* 3.8 28.5 - - + -
28A LEU* 4.2 31.6 - - + -
32A LEU* 3.6 17.9 - - + +
36A VAL* 4.2 21.8 - - + -
41A PHE* 4.4 7.9 - - + -
48A GLN* 4.6 2.5 - - - +
52A ILE* 4.1 18.8 - - + -
73A GLY* 2.7 38.6 + - - +
74A THR 4.1 1.8 - - - +
76A SER* 1.3 74.0 - - - +
78A ALA* 1.3 63.7 + - - +
80A LEU* 3.5 1.4 + - - +
81A GLN* 3.3 16.3 + - - +
112A LEU* 4.4 11.4 - - + -
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Residues in contact with ALA 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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52A ILE* 4.1 4.9 - - + +
55A ILE* 3.5 36.8 - - + -
56A ILE* 4.0 19.6 - - + +
74A THR 3.1 18.4 + - - +
75A PHE 3.9 2.5 - - - +
77A ILE* 1.3 81.0 - - - +
79A ALA* 1.3 62.1 + - - +
81A GLN* 3.4 5.0 + - - +
82A ARG* 3.3 24.8 + - - +
165A MET* 4.6 1.6 - - - -
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Residues in contact with ALA 79 (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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75A PHE 2.9 22.8 + - - +
76A SER 3.3 1.8 + - - +
78A ALA* 1.3 72.7 - - - +
80A LEU* 1.3 63.2 + - - +
82A ARG* 3.1 13.2 + - - +
83A ILE* 3.1 18.5 + - - +
92A ALA* 4.3 7.6 - - + -
94A MET* 3.4 26.5 - - + -
141A ILE* 4.6 2.9 - - + -
165A MET* 3.7 28.1 - - + +
167A ILE* 4.1 0.9 - - + -
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Residues in contact with LEU 80 (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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29A ASP* 5.9 1.4 - - - +
32A LEU* 3.7 21.2 - - + +
76A SER 3.1 21.8 + - - +
77A ILE 3.8 0.4 - - - +
79A ALA* 1.3 77.2 - - - +
81A GLN* 1.3 60.3 + - - +
83A ILE* 3.5 21.0 + - - +
109A VAL* 3.7 18.8 - - + +
112A LEU* 3.6 31.2 - - + -
113A ALA* 3.8 12.3 - - + -
116A MET* 3.7 28.0 - - + +
118A ILE* 3.8 18.9 - - + +
141A ILE* 3.7 21.3 - - + -
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Residues in contact with GLN 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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27A GLU 4.2 8.5 + - - -
28A LEU* 3.2 10.0 - - + -
29A ASP* 2.7 41.2 + - - +
32A LEU* 3.3 13.3 - - + +
56A ILE* 3.9 38.8 - - + +
77A ILE 3.3 10.7 + - - +
78A ALA 3.5 10.1 - - - +
79A ALA 3.1 0.2 - - - -
80A LEU* 1.3 81.1 - - - +
82A ARG* 1.3 58.7 + - + +
83A ILE 4.2 3.8 - - - +
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Residues in contact with ARG 82 (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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55A ILE 4.0 3.4 - - - -
56A ILE* 3.8 29.1 + - + +
58A GLY* 4.6 9.5 - - - +
78A ALA 3.3 11.8 + - - +
79A ALA 3.1 8.1 + - - +
81A GLN* 1.3 77.6 - - - +
83A ILE* 1.3 64.9 + - - +
84A ASP* 3.5 1.6 + - - +
164A LYS* 3.2 66.7 + - - +
165A MET* 4.1 12.9 - - + +
195A GLN* 3.0 41.1 - - - +
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Residues in contact with ILE 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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79A ALA 3.1 16.1 + - - +
80A LEU* 3.6 15.8 - - - +
81A GLN 3.3 4.9 - - - +
82A ARG* 1.3 79.0 - - - +
84A ASP* 1.3 63.1 + - - +
85A THR* 3.5 15.7 + - - +
91A GLN* 3.6 22.0 - - + +
92A ALA* 4.4 6.5 - - + -
118A ILE* 3.6 23.6 - - + +
140A GLN* 3.3 41.5 - - + +
141A ILE* 3.7 22.4 - - + -
164A LYS* 4.4 0.4 - - - +
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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