Contacts of the strand formed by residues 76 - 81 (chain A) in PDB entry 6N8P
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 VAL 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER* 2.4 30.0 + - - -
37A ALA* 3.3 9.0 - - + +
50A GLY* 3.9 9.4 - - - -
51A THR 3.1 15.1 + - - +
54A GLY 3.9 14.4 - - - -
55A ALA 3.9 9.2 - - - +
56A ILE* 3.9 11.0 - - + -
70A HIS* 3.8 13.7 - - + -
75A ALA* 1.3 69.9 - - - +
77A THR* 1.3 61.3 + - - +
78A GLN 4.0 7.9 - - - +
79A ILE* 3.9 27.6 - - + -
90A THR* 4.2 5.8 - - - -
91A LEU 4.2 3.1 - - - +
92A LEU* 3.7 21.3 - - + -
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Residues in contact with THR 77 (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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36A SER* 3.7 9.4 - - - +
37A ALA* 3.6 11.5 - - - +
75A ALA* 3.7 7.4 - - + +
76A VAL* 1.3 74.4 - - - +
78A GLN* 1.3 65.7 + - - +
91A LEU* 2.6 43.0 + - - +
92A LEU 3.8 0.9 - - - -
93A ASP* 3.5 36.3 - - + +
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Residues in contact with GLN 78 (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 ALA* 4.2 1.6 - - - -
38A LEU 5.7 0.2 - - - -
76A VAL* 4.0 1.0 - - - +
77A THR* 1.3 92.3 + - - +
79A ILE* 1.3 65.9 + - - +
80A HIS* 2.8 32.8 + - + +
90A THR* 3.3 6.6 - - - -
91A LEU* 3.0 45.4 + - + +
132A ILE 5.1 0.6 + - - -
133A THR 2.8 30.3 + - - -
134A VAL* 4.5 0.8 - - - +
135A VAL* 3.4 15.4 + - - +
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Residues in contact with ILE 79 (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 ALA* 3.8 13.2 - - + +
38A LEU 3.8 14.6 + - - +
39A GLY* 3.8 13.9 - - - +
48A ALA* 3.7 26.5 - - + +
49A ILE 3.7 15.0 - - - +
50A GLY* 3.4 34.3 - - - +
56A ILE* 4.3 9.9 - - + -
76A VAL* 3.9 7.4 - - + -
78A GLN* 1.3 78.7 - - - +
80A HIS* 1.3 70.4 + - - +
81A LEU* 3.8 13.4 + - + -
88A LEU* 4.7 16.4 - - + -
89A VAL 3.7 2.9 - - - -
90A THR* 4.5 4.7 - - + -
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Residues in contact with HIS 80 (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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78A GLN* 2.8 39.5 + - + +
79A ILE* 1.3 81.4 + - - +
81A LEU* 1.3 63.0 + - - +
82A LEU* 3.5 4.7 + - - +
88A LEU* 3.2 3.4 - - - -
89A VAL* 2.8 48.2 + - + +
91A LEU* 6.0 0.9 - - + -
134A VAL* 6.3 0.4 - - + -
135A VAL* 3.4 35.3 + - + +
137A PRO* 3.9 26.6 - - + +
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Residues in contact with LEU 81 (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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39A GLY* 3.8 7.0 - - - -
40A TYR* 3.4 33.5 + - - +
41A SER* 3.6 36.5 + - - +
42A PRO* 5.6 2.6 - - - +
44A LEU* 5.4 6.1 - - + -
46A ILE* 4.4 18.6 - - + +
48A ALA* 3.9 8.3 - - + -
58A LEU* 5.1 2.9 - - + -
79A ILE* 3.8 17.3 - - + -
80A HIS* 1.3 71.5 - - - +
82A LEU* 1.3 66.9 + - - +
83A PRO* 3.6 3.1 - - - +
85A GLN 5.5 1.3 - - - +
87A GLN 3.5 9.0 - - - +
88A LEU* 3.8 24.0 - - + -
137A PRO* 5.7 1.6 - - - +
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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