Contacts of the strand formed by residues 87 - 95 (chain A) in PDB entry 7EHH
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 LEU 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.8 27.4 - - + -
26A ILE* 3.8 20.6 - - + -
42A ALA* 3.9 9.6 - - + -
43A GLY* 3.5 31.4 - - - +
45A PRO* 3.8 3.9 - - - +
80A VAL* 4.0 19.1 - - + -
82A GLU* 4.3 11.4 - - + +
86A ARG* 1.3 77.0 - - - +
88A ALA* 1.3 63.3 + - - +
89A TYR* 4.1 7.4 - - + -
124A ARG* 3.3 7.1 - - - -
125A MET* 2.9 43.5 + - + +
126A PRO 4.4 0.2 + - - -
128A PHE* 3.8 15.7 - - + -
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Residues in contact with ALA 88 (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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41A LEU 3.8 0.2 - - - +
42A ALA* 3.1 4.0 - - - +
43A GLY 2.8 33.5 + - - +
45A PRO* 3.6 28.7 - - + +
57A PHE* 3.8 6.0 - - + -
87A LEU* 1.3 73.6 - - - +
89A TYR* 1.3 61.4 + - - +
119A MET 4.4 1.3 - - - +
122A TYR* 3.7 26.9 - - + -
123A PHE 3.2 7.2 - - - +
124A ARG* 4.3 5.4 - - - +
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Residues in contact with TYR 89 (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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9A HIS* 2.5 43.5 + + - -
11A PRO* 3.8 7.8 - - - +
16A ALA* 3.4 14.1 - - + +
26A ILE* 3.9 22.7 - - + -
40A LEU* 4.0 8.3 - - + -
41A LEU 2.9 11.9 - - - +
42A ALA* 3.7 13.9 - - + -
87A LEU* 4.1 9.2 - - + -
88A ALA* 1.3 78.6 - - - +
90A ALA* 1.3 61.4 + - - +
91A PHE* 3.9 17.9 - + - -
122A TYR* 3.4 6.3 - - - +
123A PHE* 2.9 63.9 + - + +
124A ARG 4.6 0.3 + - - -
125A MET* 3.6 26.0 - - + +
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Residues in contact with ALA 90 (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* 3.4 7.4 - - - +
41A LEU* 2.9 32.5 + - + +
89A TYR* 1.3 74.7 - - - +
91A PHE* 1.3 68.5 + - - +
102A ILE* 3.9 24.5 - - + -
103A TYR 3.6 12.1 - - - +
104A SER* 4.1 9.6 - - - -
122A TYR* 3.7 19.1 - - + -
123A PHE* 4.8 0.9 - - - -
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Residues in contact with PHE 91 (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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9A HIS* 3.6 36.1 - + + -
26A ILE* 3.6 24.0 - - + -
27A ARG 4.0 1.3 - - - -
28A LEU* 3.9 29.8 - - + -
38A VAL* 4.1 0.7 - - + -
39A GLU 3.4 2.5 - - - +
40A LEU* 3.5 17.3 - - + -
41A LEU* 5.4 0.2 - - - -
64A MET* 3.6 30.3 - - - -
89A TYR* 3.9 9.4 - + - -
90A ALA* 1.3 75.1 - - - +
92A LEU* 1.3 61.4 + - - +
93A VAL* 3.8 7.1 + - + -
101A LYS 3.7 0.9 - - - +
102A ILE* 3.2 7.8 - - - +
103A TYR* 2.8 59.8 + + + +
123A PHE* 3.8 13.9 - + - -
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Residues in contact with LEU 92 (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* 3.6 1.7 + - - +
38A VAL* 3.2 4.9 - - - -
39A GLU* 2.8 58.7 + - + +
41A LEU* 3.8 37.0 - - + +
61A PRO* 4.8 3.6 - - + -
90A ALA 4.3 0.2 + - - -
91A PHE* 1.3 71.4 - - - +
93A VAL* 1.3 61.6 + - - +
94A THR* 4.8 2.2 + - - -
100A GLN* 3.6 32.5 + - + +
101A LYS 3.6 7.0 - - - +
102A ILE* 4.5 3.8 - - + +
111A VAL* 3.5 32.8 - - + -
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Residues in contact with VAL 93 (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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4A LEU* 5.6 2.2 - - + -
7A ILE* 4.2 24.9 - - + -
28A LEU* 3.8 29.2 - - + -
30A THR* 5.1 0.7 - - + -
35A ILE* 4.3 15.3 - - + -
37A SER 3.5 3.6 - - - -
38A VAL* 4.0 10.5 - - + -
91A PHE* 4.3 8.7 - - + -
92A LEU* 1.3 75.1 - - - +
94A THR* 1.3 62.7 + - - +
95A ASP 4.3 0.2 - - - -
99A ILE 3.6 1.9 - - - +
100A GLN* 3.2 2.8 - - - +
101A LYS* 2.9 54.3 + - + +
103A TYR* 5.0 9.2 - - + -
108A PHE* 5.0 2.9 - - + -
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Residues in contact with THR 94 (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 5.4 - - - +
36A VAL* 2.6 33.8 + - + -
37A SER* 2.9 30.4 + - - +
92A LEU 4.8 1.0 + - - -
93A VAL* 1.3 72.9 + - - +
95A ASP* 1.3 63.6 + - - +
98A GLY* 4.0 18.2 - - - +
99A ILE 3.4 10.5 - - - +
100A GLN* 2.7 32.6 + - + +
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Residues in contact with ASP 95 (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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2A GLY* 2.9 36.1 + - - +
34A ASP* 3.2 18.4 - - - +
35A ILE* 3.9 12.1 - - + +
36A VAL* 3.3 14.2 - - - +
94A THR* 1.3 74.4 - - - +
96A MET* 1.3 65.2 + - - +
97A LEU* 3.2 8.5 + - - +
98A GLY* 3.1 14.4 + - - -
99A ILE* 2.6 55.5 + - - +
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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