Contacts of the helix formed by residues 58 - 71 (chain B) in PDB entry 3DVA
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 ALA 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU* 3.1 23.6 - - - +
187A PHE* 3.6 18.4 - - + -
28B GLU* 3.4 3.6 + - - -
56B PRO 3.0 7.5 + - - -
57B LEU* 1.3 75.9 - - - +
59B GLU* 1.3 61.2 + - - +
60B SER 3.3 1.1 - - - -
61B GLY* 3.1 0.5 + - - -
62B ILE* 2.9 31.8 + - - +
177C SER 3.4 18.4 - - - +
178C GLN* 3.8 7.4 - - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 2.8 29.8 - - - +
57B LEU* 4.1 2.9 - - - +
58B ALA* 1.3 69.6 - - - +
60B SER* 1.3 57.4 + - - +
62B ILE* 3.1 14.8 + - + +
63B GLY 2.9 23.6 + - - -
80B ILE* 4.3 16.2 - - + +
81B GLN 5.7 0.8 + - - +
85B PHE* 4.0 37.7 - - + +
88B GLU* 3.8 20.3 - - + +
89B VAL* 3.5 19.7 - - + +
178C GLN* 2.7 31.8 + - - +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.3 16.7 - - - +
180A ASP* 2.7 27.6 + - - -
183A GLU* 3.4 17.6 + - - -
58B ALA 3.3 0.6 - - - -
59B GLU* 1.3 77.1 - - - +
61B GLY* 1.3 58.6 + - - +
63B GLY* 3.1 2.4 + - - -
64B GLY 2.9 25.1 + - - -
88B GLU* 3.2 25.1 + - - +
89B VAL* 4.0 8.4 - - - -
91B ASP* 6.0 2.1 - - - +
92B SER* 3.7 4.2 + - - -
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 4.1 17.6 - - - +
183A GLU* 2.7 21.2 + - - -
187A PHE* 3.6 25.1 - - - -
58B ALA 3.1 4.8 + - - -
60B SER* 1.3 75.2 - - - +
62B ILE* 1.3 56.2 + - - +
64B GLY 3.8 0.5 - - - -
65B LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PHE* 4.2 5.8 - - + -
26B PHE* 3.8 11.8 - - + -
27B GLY* 4.1 9.0 - - - -
28B GLU* 3.8 28.3 - - + +
55B THR* 3.4 27.4 - - + +
56B PRO 4.5 0.4 - - - +
58B ALA 2.9 19.9 + - - +
59B GLU* 3.1 15.0 + - + +
61B GLY* 1.3 75.6 - - - +
63B GLY* 1.3 64.0 + - - +
65B LEU* 3.3 8.2 + - - +
66B ALA* 3.1 21.8 + - - +
78B PRO* 3.9 24.0 - - + +
79B GLU 4.3 14.8 - - - +
80B ILE* 5.9 4.5 - - + -
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU 2.9 10.9 + - - -
60B SER 3.1 3.8 + - - -
62B ILE* 1.3 75.4 - - - +
64B GLY* 1.3 62.8 + - - +
66B ALA* 3.2 6.5 + - - +
67B ILE* 3.1 26.7 + - - +
78B PRO* 6.0 1.1 - - - -
89B VAL* 3.9 9.2 - - - +
92B SER* 3.7 20.4 - - - -
97B MET* 3.9 7.8 - - - +
114B ILE* 6.2 1.3 - - - -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.1 39.8 - - - +
150A GLN* 3.3 9.7 - - - +
60B SER 2.9 15.3 + - - -
61B GLY 3.9 1.1 - - - -
63B GLY* 1.3 76.6 - - - +
65B LEU* 1.3 59.8 + - - +
67B ILE* 3.6 7.0 + - - +
68B GLY 3.1 17.3 + - - -
92B SER* 3.5 4.2 + - - -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE 3.8 0.6 + - - -
152A ALA* 3.8 10.1 - - + +
153A GLY* 3.6 24.1 - - - +
156A LEU* 3.8 23.1 - - + -
187A PHE* 4.3 15.3 - - + -
191A PHE* 4.0 29.2 - - + -
26B PHE* 4.1 21.8 - - + -
53B PHE* 4.3 3.4 - - + -
55B THR* 4.3 7.2 - - + -
61B GLY 2.9 18.0 + - - +
62B ILE* 3.5 5.8 - - - +
63B GLY 3.2 0.2 - - - -
64B GLY* 1.3 76.2 - - - +
66B ALA* 1.3 59.6 + - - +
68B GLY 3.6 0.2 + - - -
69B LEU* 3.0 43.5 + - + +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.7 13.6 - - + -
62B ILE 3.1 8.5 + - - +
63B GLY* 3.2 8.3 + - - +
65B LEU* 1.3 75.8 - - - +
67B ILE* 1.3 64.4 + - - +
69B LEU 3.5 0.2 + - - -
70B ALA* 3.0 25.3 + - - +
76B PRO* 3.3 13.7 - - + +
78B PRO* 3.6 31.6 - - + -
97B MET* 4.7 2.7 - - + -
112B ILE* 3.6 13.6 - - + +
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLN* 3.8 31.9 - - + +
63B GLY 3.1 17.7 + - - +
64B GLY 3.8 4.5 - - - +
66B ALA* 1.3 75.2 - - - +
68B GLY* 1.3 62.7 + - - +
70B ALA* 3.2 4.9 + - - +
71B LEU* 3.1 27.7 + - + +
92B SER* 3.7 20.2 - - - +
96B GLN* 3.6 29.4 - - + -
97B MET* 3.8 20.9 - - + +
100B ILE* 3.7 25.6 - - + -
110B MET* 3.7 8.0 - - + +
112B ILE* 4.1 0.2 - - - -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLN 3.5 10.7 + - - -
153A GLY* 3.5 8.3 - - - -
154A VAL* 3.4 35.7 - - - +
64B GLY 3.1 8.5 + - - -
67B ILE* 1.3 79.2 - - - +
69B LEU* 1.3 62.3 + - - +
71B LEU* 3.2 16.8 + - - +
72B GLN* 3.4 7.8 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLY 3.5 5.3 + - - +
156A LEU* 4.0 19.3 - - + -
157A GLY* 3.7 29.8 - - - +
160A MET* 4.0 10.3 - - - -
24B LEU* 4.2 10.3 - - + -
26B PHE* 3.8 31.4 - - + -
53B PHE* 4.8 1.8 - - + -
65B LEU* 3.0 34.1 + - + +
66B ALA 4.0 3.1 - - - +
68B GLY* 1.3 76.1 - - - +
70B ALA* 1.3 62.2 + - - +
72B GLN* 3.1 8.7 + - - +
74B PHE* 3.1 44.5 + - + +
76B PRO* 4.3 3.8 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA 3.0 18.8 + - - +
67B ILE 3.2 6.3 + - - +
69B LEU* 1.3 76.6 - - - +
71B LEU* 1.3 60.9 + - - +
72B GLN 3.1 0.7 - - - -
73B GLY* 3.2 13.5 + - - -
74B PHE 3.6 11.9 + - - +
76B PRO* 4.0 10.3 - - + +
109B HIS 4.4 5.7 - - - +
110B MET* 3.5 22.7 - - + -
111B PRO* 4.0 18.8 - - + +
112B ILE* 4.2 2.7 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 4.3 13.3 - - + -
99A LEU* 5.1 0.7 - - + -
138A LEU* 3.8 38.6 - - + -
150A GLN* 5.1 0.9 - - + +
154A VAL* 3.8 23.6 - - + -
67B ILE* 3.1 22.9 + - + +
68B GLY* 3.2 9.4 + - - +
70B ALA* 1.3 76.4 - - - +
72B GLN* 1.3 65.8 + - + +
73B GLY 3.4 2.1 + - - -
100B ILE* 4.9 2.9 - - + -
108B TYR* 3.5 45.7 - - + -
109B HIS 5.6 0.2 - - - -
110B MET* 3.8 17.0 - - + -
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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