Contacts of the strand formed by residues 85 - 92 (chain A) in PDB entry 3H44
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 LYS 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 2.6 24.6 + - - +
84A ASP* 1.3 83.9 - - + +
86A SER* 1.3 64.2 + - - +
135A ALA 3.4 22.1 + - - +
152A ASP* 3.8 28.7 + - + +
153A VAL 3.2 15.9 - - - +
154A SER* 4.7 1.6 - - - -
259A LEU* 4.0 0.7 - - - +
430A PRO* 3.8 16.6 - - + +
891A ILE* 4.8 11.7 - - + -
892A ARG* 4.8 16.5 + - - +
895A ASP* 3.3 31.6 + - - +
2001A DIO 3.6 6.9 - - - -
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Residues in contact with SER 86 (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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83A THR* 4.1 0.5 - - - +
85A LYS* 1.3 72.0 - - - +
87A SER* 1.3 62.7 + - - +
152A ASP* 3.2 7.3 - - - +
153A VAL* 3.0 35.0 + - - +
155A HIS* 3.3 32.4 + - - +
158A LEU* 3.6 22.6 - - - +
259A LEU* 3.2 14.4 - - - -
260A GLY* 3.1 19.7 - - - -
261A ARG 3.9 1.0 + - - -
262A GLU* 4.5 0.2 + - - -
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Residues in contact with SER 87 (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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86A SER* 1.3 78.0 - - - +
88A ALA* 1.3 63.8 + - - +
151A PHE* 2.9 21.5 + - - -
152A ASP* 4.1 2.0 - - - +
158A LEU* 4.3 2.5 - - - +
258A VAL* 3.6 2.3 - - - +
259A LEU* 2.9 34.7 + - - +
430A PRO* 3.4 28.9 + - - -
431A ARG* 3.5 5.6 - - - -
434A THR* 2.8 28.3 + - - +
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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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87A SER* 1.3 78.9 + - - +
89A ALA* 1.3 62.2 + - - +
150A TYR* 3.3 2.9 - - - +
151A PHE* 3.1 55.7 + - + +
158A LEU* 5.1 1.1 - - + -
162A LEU* 3.9 11.4 - - + -
165A PHE* 4.6 3.8 - - + -
256A VAL* 5.3 0.7 - - + -
257A VAL 3.1 13.7 - - - +
258A VAL* 3.7 18.2 - - + -
434A THR* 3.8 4.0 + - - -
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Residues in contact with ALA 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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88A ALA* 1.3 75.5 - - - +
90A LEU* 1.3 61.0 + - - +
148A ASN* 4.7 1.3 - - - +
149A TYR 3.0 12.3 - - - +
150A TYR* 3.7 5.8 - - + -
165A PHE* 4.3 4.7 - - - -
256A VAL* 3.3 9.2 - - - +
257A VAL 3.0 30.2 + - - +
434A THR* 3.5 10.1 - - - +
435A SER* 3.5 35.7 - - - +
438A ALA* 4.1 5.2 - - + +
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Residues in contact with LEU 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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73A ILE* 5.7 0.2 - - + -
89A ALA* 1.3 75.4 - - - +
91A ASP* 1.3 65.0 + - - +
92A VAL* 3.7 19.5 - - + -
147A THR 3.6 1.9 - - - +
148A ASN* 3.3 3.6 - - - -
149A TYR* 2.7 41.1 + - - -
165A PHE* 3.9 8.3 - - + -
169A PHE* 3.7 47.1 - - + -
254A MET* 3.8 26.2 - - + -
255A ALA 3.2 10.3 - - - +
256A VAL* 3.8 20.0 - - + -
275A PHE* 3.9 22.0 - - + -
438A ALA* 4.5 1.8 - - - -
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Residues in contact with ASP 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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90A LEU* 1.3 76.0 - - - +
92A VAL* 1.3 62.3 + - - +
141A PHE* 5.3 0.9 - - - -
146A HIS* 2.6 37.8 + - - +
147A THR 3.3 3.4 - - - +
148A ASN* 2.9 29.1 - - - +
254A MET* 3.3 3.1 - - - -
255A ALA 2.8 33.6 + - - +
438A ALA* 3.4 29.3 - - + +
439A GLY* 3.9 6.9 - - - -
442A HIS* 2.9 22.4 + - - +
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Residues in contact with VAL 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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90A LEU* 3.7 19.1 - - + -
91A ASP* 1.3 76.5 - - - +
93A HIS* 1.3 59.9 + - - +
94A ILE* 2.8 21.5 + - + +
146A HIS* 3.3 4.2 - - - -
147A THR* 2.8 33.4 + - - +
149A TYR* 4.6 2.7 - - + -
248A TYR 4.1 20.2 - - - +
249A TYR* 3.7 37.5 - - + +
253A LEU* 3.3 16.8 - - + +
254A MET* 4.0 15.5 - - + -
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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