Contacts of the strand formed by residues 163 - 172 (chain A) in PDB entry 1A7C
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 5.3 0.7 - - + -
49A THR* 4.5 7.4 - - + +
97A ILE* 3.4 38.6 - - + -
98A PHE 3.4 7.2 - - - +
99A VAL* 4.3 7.6 - - + -
126A PHE* 4.6 0.2 - - - -
161A THR* 3.9 1.2 - - - +
162A ARG* 1.3 81.6 - - + +
164A VAL* 1.3 70.5 + - - +
165A LEU* 4.0 19.7 - - + -
306A PHE* 4.2 15.5 - - + -
309A LEU* 3.8 29.6 - - + -
315A LEU* 4.9 2.5 - - + -
911C THR 3.8 0.4 - - - +
912C VAL* 3.5 0.5 - - - +
913C ALA* 2.7 53.1 + - + +
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Residues in contact with VAL 164 (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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97A ILE* 3.5 3.6 - - - -
98A PHE* 2.9 41.8 + - + +
126A PHE* 3.7 24.9 - - + -
136A ILE* 3.9 25.6 - - + -
152A LEU* 4.3 12.3 - - + -
157A VAL* 4.3 4.3 - - + -
161A THR* 4.0 8.7 - - + -
163A LEU* 1.3 79.2 - - - +
165A LEU* 1.3 65.1 + - - +
166A VAL* 4.0 20.9 - - + -
910C ACE 5.2 0.2 - - - -
911C THR 3.3 10.1 - - - +
912C VAL* 4.3 15.0 - - + -
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Residues in contact with LEU 165 (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 VAL* 4.1 18.8 - - + +
45A MET* 4.1 21.8 - - + +
46A LEU* 3.5 50.3 - - + +
49A THR* 4.7 5.4 - - + +
96A ALA 3.6 2.7 - - - +
97A ILE* 3.4 41.7 - - + -
163A LEU* 4.0 14.8 - - + -
164A VAL* 1.3 72.3 - - - +
166A VAL* 1.3 65.4 + - - +
910C ACE 3.9 0.7 - - - +
911C THR* 2.9 38.8 + - + +
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Residues in contact with VAL 166 (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 VAL* 4.5 2.9 - - - -
45A MET* 3.5 7.6 - - - +
94A THR 4.0 0.2 - - - +
95A ASP* 3.4 2.3 - - - -
96A ALA* 2.9 36.2 + - + +
98A PHE* 3.8 23.6 - - + -
136A ILE* 4.6 6.1 - - + -
139A TRP* 3.7 25.1 - - + -
140A VAL* 4.6 4.7 - - + -
151A LEU* 3.8 27.8 - - + -
164A VAL* 4.0 15.3 - - + -
165A LEU* 1.3 80.4 - - - +
167A ASN* 1.3 62.2 + - - +
168A ALA 4.2 0.2 - - - -
910C ACE 4.0 10.1 - - + -
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Residues in contact with ASN 167 (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 TYR* 4.6 1.1 - - - -
38A GLY* 3.5 22.6 - - - +
41A SER* 3.8 16.1 + - - -
42A VAL* 3.9 22.6 - - + +
93A THR* 3.1 25.2 + - - -
94A THR 3.4 6.6 + - - -
95A ASP* 2.8 24.7 + - - +
140A VAL* 6.0 1.4 - - - +
151A LEU* 6.1 0.3 - - - +
166A VAL* 1.3 77.8 - - - +
168A ALA* 1.3 58.5 + - - +
169A LEU* 3.8 15.8 - - - +
905B SER* 3.6 15.6 + - - +
906B NH2 4.2 2.4 + - - -
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Residues in contact with ALA 168 (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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92A SER 3.6 1.4 - - - +
93A THR* 3.2 6.1 + - - -
94A THR* 2.8 36.3 + - - +
139A TRP* 3.8 16.6 - - + -
140A VAL* 4.9 6.3 - - + +
143A HIS* 3.7 36.1 - - + +
144A THR* 4.2 9.0 - - + -
166A VAL 4.2 0.2 - - - -
167A ASN* 1.3 73.8 - - - +
169A LEU* 1.3 59.4 + - - +
905B SER 3.6 4.9 - - - -
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Residues in contact with LEU 169 (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 SER* 3.3 26.2 - - - +
37A TYR* 4.2 17.3 - - + -
38A GLY 4.6 1.1 - - - +
91A ILE* 4.3 16.4 - - + -
92A SER 3.4 12.1 - - - +
93A THR* 3.8 17.5 - - + +
144A THR* 4.1 2.3 - - - +
167A ASN* 3.8 11.6 - - - +
168A ALA* 1.3 74.9 - - - +
170A TYR* 1.3 63.0 + - - +
171A PHE* 6.0 0.4 - - + -
371A LEU* 3.9 21.1 - - + +
372A PHE* 3.6 24.2 - - + -
904B SER* 3.0 8.0 + - - -
905B SER* 2.8 40.3 + - - +
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Residues in contact with TYR 170 (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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90A GLU* 3.7 28.4 + - + -
91A ILE* 3.3 6.9 - - - +
92A SER* 2.8 47.7 + - - +
143A HIS 4.1 15.5 - - - +
144A THR* 3.6 12.6 - - - -
145A LYS* 3.7 39.5 + - + +
147A MET* 4.2 15.3 - - + -
169A LEU* 1.3 78.2 - - - +
171A PHE* 1.3 62.4 + - - +
172A ASN* 3.5 34.5 + - + +
902B VAL* 4.2 10.3 - - + +
903B ALA 3.5 2.0 - - - -
904B SER* 3.2 21.8 - - - +
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Residues in contact with PHE 171 (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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89A ASP* 4.2 3.1 - - + -
90A GLU 3.3 16.4 - - - -
91A ILE* 3.9 14.4 - - + -
169A LEU* 5.8 0.7 - - + -
170A TYR* 1.3 77.5 - - - +
172A ASN* 1.3 61.7 + - - +
173A GLY* 3.9 20.4 - - - -
228A TYR* 3.7 35.0 - + - -
233A LEU* 4.1 25.8 - - + -
362A VAL* 3.9 21.3 - - + -
371A LEU* 5.2 2.7 - - + -
372A PHE* 3.7 21.5 - + + -
901B THR* 3.8 30.7 - - + -
902B VAL* 3.3 6.8 - - - +
903B ALA* 2.7 44.1 + - + +
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Residues in contact with ASN 172 (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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89A ASP* 3.8 1.4 - - - -
90A GLU* 2.9 49.4 + - + +
170A TYR* 3.5 32.1 + - + +
171A PHE* 1.3 76.0 - - - +
173A GLY* 1.3 64.5 + - - +
333A THR* 4.0 32.0 + - - +
901B THR 3.5 2.7 - - - +
902B VAL* 3.8 19.2 - - + +
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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