Contacts of the helix formed by residues 50 - 59 (chain B) in PDB entry 1VE3
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 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B CYS 3.0 15.4 + - - -
48B GLY 3.2 1.8 + - - -
49B VAL* 1.3 76.9 - - - +
51B GLY* 1.3 56.5 + - - +
52B PHE 3.2 3.1 - - - -
53B SER* 2.7 28.8 + - - -
54B PHE* 2.9 17.9 + - - -
76B ALA* 4.2 0.2 - - - +
89B PHE* 3.8 24.5 - - - -
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Residues in contact with GLY 51 (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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16B ILE* 3.4 24.0 - - - +
21B TYR* 3.1 26.2 + - - -
25B ILE* 4.2 12.2 - - - +
50B GLY* 1.3 74.0 - - - +
52B PHE* 1.3 56.8 + - - +
54B PHE* 3.6 6.6 + - - +
55B LEU* 3.1 25.5 + - - +
83B ARG* 5.4 1.3 + - - -
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Residues in contact with PHE 52 (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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21B TYR* 4.7 2.2 - + - -
24B ARG* 3.6 20.9 - - - -
25B ILE* 3.9 39.3 - - + -
28B LEU* 3.9 31.0 - - + -
32B LEU* 4.2 12.8 - - + -
44B ASP* 3.9 11.7 - - - +
47B CYS 5.5 1.2 + - - -
50B GLY 3.2 1.0 - - - -
51B GLY* 1.3 74.5 - - - +
53B SER* 1.3 65.5 + - - +
55B LEU* 3.5 13.5 - - + +
56B LEU* 3.1 31.8 + - - +
108B ILE* 4.1 12.6 - - + -
110B ILE* 3.6 22.0 - - + -
301B SAM 3.3 35.0 - - - -
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Residues in contact with SER 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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44B ASP* 2.7 34.1 + - - +
47B CYS* 4.2 0.7 - - - +
50B GLY 2.7 15.2 + - - -
52B PHE* 1.3 74.3 - - - +
54B PHE* 1.3 57.1 + - - -
56B LEU* 3.1 5.9 + - - +
57B GLU* 2.9 28.4 + - - +
63B VAL* 3.5 24.0 - - - +
65B GLY* 4.2 1.0 - - - -
87B VAL* 3.9 16.2 - - - -
89B PHE* 3.9 16.7 - - - -
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Residues in contact with PHE 54 (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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16B ILE* 3.8 9.2 - - + -
49B VAL 3.6 20.4 - - - -
50B GLY 2.9 22.4 + - - +
51B GLY* 3.9 3.8 - - - +
53B SER* 1.3 72.5 - - - +
55B LEU* 1.3 66.5 + - - +
57B GLU* 3.6 6.4 - - - +
58B ASP* 3.0 32.5 + - - +
76B ALA 3.5 22.4 - - - -
79B TYR* 3.6 15.7 - - + -
80B ALA* 3.6 11.0 - - + -
83B ARG* 3.8 32.8 - - - +
85B SER* 3.4 38.1 - - - -
87B VAL* 4.1 3.4 - - + -
89B PHE* 3.6 22.7 - + - -
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Residues in contact with LEU 55 (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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25B ILE* 4.0 26.0 - - + +
29B GLU* 3.8 35.7 - - + +
32B LEU* 4.8 7.6 - - + -
33B MSE 5.9 2.2 - - + -
51B GLY 3.1 15.4 + - - +
52B PHE* 3.5 24.5 - - + +
54B PHE* 1.3 76.5 - - - +
56B LEU* 1.3 67.5 + - + +
58B ASP* 3.2 19.9 + - + +
59B TYR* 3.1 47.2 + - + -
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Residues in contact with LEU 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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32B LEU* 5.0 7.9 - - + -
33B MSE 3.7 31.2 - - + -
36B MSE 4.1 16.2 - - + -
42B VAL* 3.5 31.9 - - + -
52B PHE 3.1 17.3 + - - +
53B SER* 3.6 5.8 - - - +
55B LEU* 1.3 80.6 - - + +
57B GLU* 1.3 64.3 + - - +
59B TYR* 3.0 10.9 + - + +
61B PHE* 3.1 32.3 + - + -
63B VAL* 3.7 13.5 - - + -
108B ILE* 3.9 20.6 - - + -
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Residues in contact with GLU 57 (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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53B SER 2.9 15.9 + - - +
54B PHE* 3.6 9.7 - - - +
56B LEU* 1.3 76.1 - - - +
58B ASP* 1.3 64.5 + - - +
60B GLY* 2.9 20.3 + - - -
61B PHE 3.9 13.8 + - - +
63B VAL* 3.8 3.8 - - + +
85B SER* 2.5 30.1 + - - -
86B ASN* 2.5 40.0 + - - +
87B VAL* 3.3 14.3 + - + +
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Residues in contact with ASP 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 PHE* 3.0 23.7 + - - +
55B LEU* 3.2 15.6 + - + +
57B GLU* 1.3 81.9 - - - +
59B TYR* 1.3 63.9 + - + +
60B GLY 3.3 1.1 + - - -
83B ARG* 5.5 2.9 + - - -
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Residues in contact with TYR 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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29B GLU* 2.5 27.8 + - + +
33B MSE 4.1 31.9 - - + +
39B ARG* 2.7 46.4 + - - +
55B LEU* 3.1 47.1 + - + -
56B LEU* 3.0 10.2 + - - +
57B GLU 3.0 1.2 - - - -
58B ASP* 1.3 83.7 - - + +
60B GLY* 1.3 56.5 + - - +
61B PHE* 3.5 15.7 - - + -
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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