Contacts of the strand formed by residues 34 - 40 (chain I) in PDB entry 1V7M
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 MET 34 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 3.7 18.2 - - + -
27I PHE* 4.8 1.8 - - - -
29I PHE* 3.8 30.3 - - + -
32I ALA* 4.1 11.2 - - - +
33I TRP* 1.3 83.1 - - - +
35I ASP* 1.3 71.6 + - - +
36I TRP* 5.9 0.7 - - - -
50I GLU* 3.3 2.1 - - - +
51I ILE* 2.9 37.3 + - + +
74I ARG* 3.9 13.2 - - - +
81I VAL* 3.8 28.5 - - + -
98I CYS* 3.6 27.8 - - - -
99I SER 3.1 24.5 - - - +
100I GLY* 3.6 8.1 - - - -
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Residues in contact with ASP 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I TRP* 4.6 1.6 - - - +
34I MET* 1.3 90.5 + - - +
36I TRP* 1.3 66.4 + - - +
37I VAL 4.3 0.2 - - - -
47I TRP* 2.9 26.4 + - + +
49I ALA 3.2 7.6 - - - +
50I GLU* 3.4 17.8 - - - +
81I VAL* 5.9 0.5 - - - +
98I CYS* 3.7 2.8 - - - -
99I SER* 2.9 39.8 + - - +
102I SER* 4.0 16.5 + - - -
103I PHE* 3.1 40.3 + - + -
95M ARG* 5.1 0.3 - - - -
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Residues in contact with TRP 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLU* 4.2 7.9 - - + -
20I LEU* 3.9 29.2 - - + -
21I SER 4.0 13.9 - - - -
22I CYS* 4.1 7.0 - - + -
34I MET 5.9 0.4 - - - -
35I ASP* 1.3 77.1 - - - +
37I VAL* 1.3 56.0 + - - +
47I TRP* 3.9 1.6 - - - -
48I VAL* 2.6 50.6 + - + +
49I ALA* 2.9 13.3 + - + +
72I VAL* 4.0 20.9 - - + -
81I VAL* 3.7 41.9 - - + +
82I TYR 3.5 15.6 + - - -
83I LEU* 3.9 33.0 - - + -
96I TYR* 4.5 12.6 - + + -
97I TYR 3.5 21.5 - - - -
98I CYS* 3.7 16.8 - - + -
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Residues in contact with VAL 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ASP* 4.7 1.8 - - + -
36I TRP* 1.3 79.2 - - - +
38I ARG* 1.3 70.1 + - - +
45I LEU* 4.5 10.3 - - + -
46I GLU 3.6 18.2 - - - +
47I TRP* 4.3 7.9 - - + -
48I VAL* 4.3 0.4 - - - +
96I TYR* 3.7 0.8 - - - -
97I TYR* 2.8 39.5 + - + +
99I SER* 5.0 2.0 - - - -
103I PHE* 3.6 31.2 - - + -
106I TRP* 3.9 32.5 - - + -
97M PHE* 4.2 13.5 - - + -
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Residues in contact with ARG 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I VAL* 1.3 77.1 - - - +
39I GLN* 1.3 65.3 + - - +
40I SER* 6.1 0.2 - - - +
44I GLY 3.6 1.0 - - - +
45I LEU* 3.9 2.1 - - - -
46I GLU* 2.8 81.3 + - + +
48I VAL* 3.5 18.2 - - + +
65I SER* 4.4 8.3 + - - -
66I VAL* 4.2 17.9 - - - +
70I PHE* 4.2 6.7 - - - -
91I GLU 4.4 2.4 + - - -
92I ASP* 2.9 50.5 + - - +
93I THR 5.7 1.8 - - - +
94I GLY* 5.6 1.8 - - - -
95I ILE 3.1 10.3 - - - +
96I TYR* 3.3 41.1 + - + -
97I TYR* 5.2 0.2 - - - -
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Residues in contact with GLN 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ARG* 1.3 78.8 - - - +
40I SER* 1.3 70.1 + - - +
44I GLY* 3.6 11.0 - - - +
45I LEU* 3.2 26.4 - - + +
46I GLU* 5.8 0.2 - - - -
94I GLY* 3.4 8.3 - - - -
95I ILE* 2.9 43.1 + - + +
97I TYR* 3.4 23.4 + - + -
37M GLN* 2.9 42.5 - - - +
86M TYR* 3.7 12.3 + - - -
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Residues in contact with SER 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ARG* 6.1 0.5 - - - +
39I GLN* 1.3 82.1 - - - +
41I PRO* 1.3 74.2 - - - +
42I GLU* 3.1 16.9 + - - -
43I LYS* 3.2 29.3 + - - +
44I GLY* 2.9 24.7 + - - -
46I GLU* 5.1 2.3 + - - +
91I GLU 5.7 0.3 + - - -
93I THR 4.2 15.5 + - - -
94I GLY* 5.1 0.7 - - - -
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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