Contacts of the strand formed by residues 35 - 43 (chain A) in PDB entry 7EHI
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 ILE 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLY* 5.2 2.2 - - - -
4A LEU* 6.1 0.4 - - + -
7A ILE* 4.1 18.6 - - + -
30A THR* 3.7 33.8 + - + +
31A ALA 4.2 1.6 + - - -
33A ASP* 4.6 2.6 - - - -
34A ASP* 1.3 102.9 + - - +
36A VAL* 1.3 61.5 + - - +
37A SER 3.3 27.1 - - - +
38A VAL* 3.6 19.3 - - + -
66A LYS* 4.6 8.7 + - - -
74A ASP* 4.9 1.1 + - - +
76A TRP* 3.4 15.7 - - + -
93A VAL* 4.5 10.8 - - + -
94A THR 3.5 6.3 - - - +
95A ASP* 3.8 19.5 - - + +
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Residues in contact with VAL 36 (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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35A ILE* 1.3 72.8 - - - +
37A SER* 1.3 62.4 + - - +
76A TRP* 3.6 11.8 - - - -
94A THR* 2.8 15.9 + - + +
95A ASP 3.4 21.8 - - - +
96A MET* 3.5 35.7 - - + +
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Residues in contact with SER 37 (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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35A ILE* 3.3 7.4 - - - +
36A VAL* 1.3 84.5 - - - +
38A VAL* 1.3 66.4 + - - +
39A GLU* 5.7 2.4 - - - +
63A GLN* 4.2 16.4 - - - +
76A TRP* 4.0 5.4 - - - -
92A LEU 3.8 1.0 + - - +
93A VAL* 3.7 0.3 - - - -
94A THR* 3.1 45.2 + - - +
100A GLN* 5.4 0.3 + - - -
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Residues in contact with VAL 38 (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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28A LEU* 3.8 24.5 - - + -
35A ILE* 3.6 15.5 - - + -
37A SER* 1.3 81.1 - - - +
39A GLU* 1.3 72.8 + - - +
63A GLN* 4.0 4.0 + - - +
64A MET* 2.9 53.2 + - + +
76A TRP* 3.6 39.2 - - + +
91A PHE* 4.1 4.5 - - + -
92A LEU 3.3 8.5 - - - +
93A VAL* 4.2 6.3 - - + -
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Residues in contact with GLU 39 (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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37A SER* 5.7 2.7 - - - +
38A VAL* 1.3 80.5 - - - +
40A LEU* 1.3 59.0 + - - +
61A PRO* 3.4 35.0 - - + +
62A LYS 3.3 8.5 - - - +
63A GLN* 2.8 33.7 + - - +
64A MET* 4.4 0.4 - - - -
91A PHE* 3.5 4.5 - - - -
92A LEU* 2.8 53.2 + - + +
100A GLN* 5.6 2.9 + - - -
604A MES 5.5 1.0 - - - +
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Residues in contact with LEU 40 (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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26A ILE* 4.0 12.8 - - + -
39A GLU* 1.3 73.4 - - - +
41A LEU* 1.3 63.1 + - - +
42A ALA* 3.8 19.9 + - + -
61A PRO* 3.3 4.0 - - - +
62A LYS* 2.7 50.5 + - + +
64A MET* 4.2 10.4 - - + +
78A VAL* 3.8 11.2 - - + -
80A VAL* 3.5 32.3 - - + -
89A TYR* 4.1 11.7 - - + -
90A ALA 3.5 11.9 - - - +
91A PHE* 3.5 36.1 - - + -
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Residues in contact with LEU 41 (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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40A LEU* 1.3 70.8 - - - +
42A ALA* 1.3 60.9 + - - +
57A PHE* 4.1 6.9 - - + -
58A TYR* 3.7 42.4 - - + +
61A PRO* 3.7 31.4 - - + -
89A TYR* 3.0 4.2 - - - +
90A ALA* 2.9 40.6 + - + +
92A LEU* 3.9 29.2 - - + -
102A ILE* 3.7 30.1 - - + -
116A LEU* 4.7 8.7 - - + -
122A TYR* 4.8 3.1 - - + -
604A MES 4.2 4.0 - - - +
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Residues in contact with ALA 42 (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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40A LEU* 3.8 20.3 + - + -
41A LEU* 1.3 75.9 - - - +
43A GLY* 1.3 58.8 + - - +
57A PHE* 3.2 23.4 + - - +
60A VAL 5.5 0.2 + - - -
62A LYS* 3.3 33.0 + - + +
80A VAL* 4.7 1.3 - - + -
87A LEU* 4.1 15.0 - - + -
88A ALA 3.1 11.2 - - - +
89A TYR* 3.7 12.3 - - + -
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Residues in contact with GLY 43 (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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42A ALA* 1.3 75.3 - - - +
44A ASP* 1.3 64.2 - - - -
45A PRO* 3.3 0.3 - - - +
57A PHE* 3.5 17.9 - - - -
82A GLU* 4.2 7.6 - - - -
87A LEU* 3.5 16.2 - - - +
88A ALA* 2.8 32.6 + - - +
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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