Contacts of the helix formed by residues 52 - 71 (chain B) in PDB entry 1VGX
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 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 3.7 3.2 + - - -
51B ILE* 1.3 76.3 - - - +
53B PRO* 1.3 79.6 - - - +
54B ALA* 3.0 32.4 + - - +
55B ALA* 3.1 13.5 + - + +
56B ILE* 2.9 19.9 + - - +
83B ARG* 4.1 1.6 - - - +
132B ASP* 5.4 3.1 - - - +
135B ALA* 6.0 1.6 - - + -
139B HIS* 4.8 2.5 + - - +
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Residues in contact with PRO 53 (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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53A PRO* 3.4 29.2 - - + -
81A GLY 4.7 1.7 - - - +
83A ARG* 3.7 28.9 - - - +
51B ILE 4.4 0.4 - - - +
52B ASP* 1.3 96.7 - - - +
54B ALA* 1.3 61.1 + - - +
56B ILE* 3.4 12.3 + - + +
57B HIS* 3.0 24.8 + - - +
83B ARG* 3.7 19.3 - - - +
130B ASP* 3.8 7.5 - - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 3.0 15.1 + - - +
53B PRO* 1.3 77.0 - - - +
55B ALA* 1.3 58.5 + - - +
57B HIS* 3.2 4.7 + - - +
58B THR* 3.0 30.8 + - - -
130B ASP* 3.4 39.2 + - - +
131B HIS* 3.7 13.2 - - - +
132B ASP* 3.6 9.8 + - + +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ILE* 3.7 15.0 - - + -
52B ASP* 3.1 17.2 + - + +
54B ALA* 1.3 80.0 - - - +
56B ILE* 1.3 57.6 + - - +
58B THR* 3.3 3.1 + - - -
59B LEU* 2.9 31.4 + - - +
132B ASP* 4.1 12.9 - - + +
135B ALA* 3.8 27.6 - - + -
136B ALA* 3.9 7.1 - - - +
139B HIS* 4.2 6.1 - - + +
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Residues in contact with ILE 56 (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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81A GLY* 5.5 2.2 - - - +
51B ILE* 3.6 25.5 - - + +
52B ASP 2.9 10.7 + - - +
53B PRO* 3.6 15.3 - - + +
55B ALA* 1.3 78.3 - - - +
57B HIS* 1.3 61.0 + - - +
59B LEU* 3.6 4.4 - - + +
60B GLU* 2.8 28.9 + - - +
79B PRO* 3.8 24.2 - - + +
80B MET 4.4 0.2 - - - +
83B ARG* 3.7 44.6 - - + -
85B GLY 3.7 18.2 - - - +
86B MET* 3.6 19.4 - - - +
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Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY* 3.3 32.1 + - - +
82A CSD 3.6 16.1 + - - -
53B PRO 3.0 18.7 + - - +
54B ALA 3.3 6.3 - - - +
56B ILE* 1.3 76.8 - - - +
58B THR* 1.3 61.1 + - - +
60B GLU* 3.2 11.6 + - - +
61B HIS* 3.1 19.9 + + - -
125B CYS* 3.3 2.7 - - - -
127B ASN* 3.2 18.6 + - + -
130B ASP* 2.8 22.4 + - - +
131B HIS* 3.2 17.4 + + - -
167B ZN 2.2 35.5 - - - -
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Residues in contact with THR 58 (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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54B ALA 3.0 6.0 + - - -
55B ALA 3.6 7.0 - - - -
57B HIS* 1.3 73.5 - - - +
59B LEU* 1.3 65.9 + - - +
61B HIS* 3.2 3.7 + - - +
62B LEU* 2.9 35.3 + - + +
117B ILE* 3.5 24.0 - - + -
131B HIS* 2.9 22.1 + - - +
132B ASP 2.8 30.2 + - - -
133B LEU* 4.0 6.5 - - - -
136B ALA* 3.6 18.8 - - + -
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Residues in contact with LEU 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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43B PHE* 3.9 36.1 - - + -
51B ILE* 4.2 20.6 - - + -
55B ALA 2.9 19.4 + - - +
56B ILE* 3.6 17.5 - - + +
58B THR* 1.3 77.5 - - - +
60B GLU* 1.3 57.4 + - - +
62B LEU* 4.5 2.9 - - - +
63B LEU* 2.9 42.0 + - + +
86B MET* 4.1 11.9 - - - -
107B LEU* 5.5 0.4 - - + -
110B THR* 4.0 16.6 - - + -
136B ALA* 3.7 29.8 - - + +
139B HIS* 4.4 7.2 - - + -
140B ALA* 5.0 0.9 - - + -
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Residues in contact with GLU 60 (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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79A PRO 4.6 0.2 - - - +
80A MET* 3.9 5.5 - - - +
81A GLY* 2.9 36.7 + - - -
82A CSD 4.3 0.9 + - - -
87A TYR* 5.2 7.8 - - - -
56B ILE 2.8 14.3 + - - +
57B HIS* 3.4 20.5 + - - +
59B LEU* 1.3 77.7 - - - +
61B HIS* 1.4 70.0 + - - +
63B LEU* 5.0 0.9 - - - -
64B ALA* 3.1 26.0 + - + +
77B VAL* 3.9 20.8 - - - +
78B SER* 4.6 1.2 + - - -
79B PRO* 3.4 15.1 - - + +
86B MET* 3.6 15.8 - - + +
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Residues in contact with HIS 61 (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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57B HIS* 3.1 23.6 + + - +
58B THR 3.2 6.9 + - - +
60B GLU* 1.4 84.1 - - + +
62B LEU* 1.3 62.7 + - - +
64B ALA* 3.6 13.4 + - - +
65B GLY 4.0 3.1 + - - -
117B ILE* 3.7 14.4 - - + -
118B PRO* 2.8 30.7 + - - +
119B GLY* 3.3 25.7 - - - -
120B VAL* 3.9 3.0 - - + +
124B GLU 5.2 1.1 - - - -
125B CYS* 3.8 1.3 - - + -
131B HIS* 3.6 16.4 - + - -
167B ZN 2.0 37.7 - - - -
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Residues in contact with LEU 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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58B THR* 2.9 38.9 + - + +
59B LEU* 4.1 2.9 - - - +
61B HIS* 1.3 77.6 - - - +
63B LEU* 1.3 59.6 + - + +
65B GLY* 3.4 3.1 + - - -
66B TYR* 3.0 38.1 + - + -
110B THR* 4.0 31.9 - - + +
113B HIS* 3.7 32.5 - - + +
117B ILE* 4.5 3.6 - - + -
118B PRO* 3.6 28.3 - - + -
133B LEU* 3.9 17.0 - - + -
136B ALA* 4.5 4.3 - - + -
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Residues in contact with LEU 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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41B LEU* 5.8 0.7 - - + -
43B PHE* 4.2 17.0 - - + -
59B LEU* 2.9 31.6 + - + +
62B LEU* 1.3 70.3 - - + +
64B ALA* 1.3 66.0 + - - +
66B TYR* 4.2 2.5 - - + +
67B MET* 2.9 37.7 + - + +
77B VAL* 3.9 18.7 - - + +
86B MET* 3.9 28.3 - - + -
103B PHE* 4.6 8.1 - - + -
106B ALA* 4.0 26.5 - - + +
107B LEU* 4.7 8.5 - - + -
110B THR* 3.8 19.7 - - - +
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Residues in contact with ALA 64 (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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60B GLU* 3.1 20.9 + - + +
61B HIS* 3.7 8.5 - - - +
62B LEU 3.2 0.4 - - - -
63B LEU* 1.3 78.4 - - - +
65B GLY* 1.3 58.9 + - - +
67B MET* 4.8 0.3 - - - +
68B ARG* 2.8 46.0 + - - +
76B ASP* 5.5 2.5 - - - +
77B VAL* 4.4 12.9 - - + +
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Residues in contact with GLY 65 (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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61B HIS 4.0 3.6 + - - -
62B LEU 3.4 4.7 + - - -
63B LEU 3.2 0.4 - - - -
64B ALA* 1.3 79.5 - - - +
66B TYR* 1.3 66.5 + - - +
68B ARG* 3.2 8.9 + - - +
69B ASP* 3.1 26.5 + - - +
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Residues in contact with TYR 66 (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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62B LEU* 3.0 31.0 + - + +
63B LEU* 4.5 2.7 - - - -
65B GLY* 1.3 76.0 - - - +
67B MET* 1.3 62.4 + - - +
69B ASP* 3.3 23.4 + - - -
70B HIS* 3.2 26.7 - - - -
106B ALA* 3.6 19.5 - - + +
109B ASP* 3.5 46.7 + - + +
110B THR* 3.7 17.0 - - - -
113B HIS* 2.7 37.2 + + - +
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Residues in contact with MET 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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41B LEU* 4.6 4.5 - - + -
63B LEU* 2.9 30.0 + - + +
64B ALA 4.8 0.4 - - - +
66B TYR* 1.3 76.3 - - - +
68B ARG* 1.3 58.6 + - - +
70B HIS* 3.0 4.8 + - - +
71B LEU* 2.9 42.7 + - + +
74B VAL* 4.5 5.6 - - + -
77B VAL* 3.9 23.1 - - + -
88B MET* 3.7 34.3 - - + -
99B VAL* 4.5 2.5 - - + +
102B ALA* 4.2 5.2 - - + +
103B PHE* 3.7 43.7 - - + +
106B ALA* 3.6 21.1 - - - -
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Residues in contact with ARG 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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8A GLU* 5.2 7.5 + - - +
9A SER* 5.6 4.2 - - - -
38A LYS* 3.9 7.5 - - - +
64B ALA* 2.8 40.4 + - - +
65B GLY* 3.2 10.8 + - - +
67B MET* 1.3 78.4 - - - +
69B ASP* 1.3 60.6 + - - +
70B HIS 3.4 0.5 + - - -
71B LEU 3.5 15.6 + - - +
72B GLU* 5.5 0.5 - - - +
74B VAL* 3.9 33.6 + - + +
75B VAL 3.1 19.0 + - - -
76B ASP* 2.8 29.5 + - - +
77B VAL 5.0 1.0 - - - +
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Residues in contact with ASP 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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65B GLY 3.1 15.2 + - - +
66B TYR* 3.4 34.9 - - - +
67B MET 3.2 0.2 - - - -
68B ARG* 1.3 76.6 - - - +
70B HIS* 1.3 75.1 + - + +
109B ASP* 4.6 1.0 - - - +
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Residues in contact with HIS 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 TYR 3.2 22.4 - - - +
67B MET 3.0 3.5 + - - +
69B ASP* 1.3 89.0 + - + +
71B LEU* 1.3 62.6 + - - +
102B ALA* 3.6 28.4 - - + +
105B ALA* 3.6 31.3 - - + +
106B ALA* 3.7 7.2 - - - -
109B ASP* 2.8 29.2 + - - -
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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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67B MET* 2.9 20.0 + - + +
68B ARG* 3.5 16.0 + - - +
69B ASP 3.7 1.0 - - - -
70B HIS* 1.3 82.1 - - - +
72B GLU* 1.3 75.7 + - - +
73B GLY 4.1 0.2 + - - -
74B VAL* 3.7 22.3 - - + +
88B MET* 3.6 32.1 - - + -
90B VAL* 4.0 13.9 - - + -
95B ASP* 6.1 0.7 - - + +
98B GLY 4.9 4.5 - - - +
99B VAL* 4.3 21.8 - - + -
102B ALA* 3.9 14.8 - - + -
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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
------------------------------------------------------------
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