Contacts of the strand formed by residues 165 - 176 (chain A) in PDB entry 5BUK
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 GLN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A SER* 3.4 5.7 - - - -
162A VAL* 2.8 42.8 + - + +
163A ALA* 3.8 8.3 - - + +
164A GLY* 1.3 86.9 - - - +
166A ARG* 1.3 66.7 + - - +
167A ALA* 3.6 0.4 + - + -
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Residues in contact with ARG 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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147A ASN* 3.8 27.8 + - - +
148A ARG* 5.0 1.6 - - - +
159A GLU* 2.8 55.2 + - - +
160A THR 3.5 8.3 - - - -
161A SER* 5.0 0.4 - - - +
164A GLY 4.2 0.4 + - - -
165A GLN* 1.3 76.9 + - - +
167A ALA* 1.3 59.2 + - - +
168A LYS* 4.2 24.8 + - + +
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Residues in contact with ALA 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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158A LEU 3.5 1.2 - - - +
160A THR* 2.9 49.9 + - - +
162A VAL* 3.9 20.2 - - + -
165A GLN* 3.6 1.2 + - + -
166A ARG* 1.3 73.3 - - - +
168A LYS* 1.3 62.2 + - - +
169A VAL* 3.6 6.9 + - + +
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Residues in contact with LYS 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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157A VAL* 3.6 19.3 - - + -
158A LEU 3.5 4.9 - - - -
159A GLU* 4.5 18.2 - - + +
166A ARG* 4.1 24.8 + - + +
167A ALA* 1.3 70.7 - - - +
169A VAL* 1.3 61.1 + - - +
170A PRO* 3.4 11.5 - - - +
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Residues in contact with VAL 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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5A PHE* 5.0 13.0 - - + -
31A ALA* 5.2 1.3 - - + -
33A PHE* 3.9 33.9 - - + -
157A VAL* 3.8 1.8 - - - +
158A LEU* 2.8 43.7 + - + +
160A THR* 4.3 7.4 - - + +
167A ALA* 4.0 13.7 - - + +
168A LYS* 1.3 74.8 - - - +
170A PRO* 1.3 76.7 - - + +
171A VAL* 3.5 13.4 + - + +
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Residues in contact with PRO 170 (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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3A PRO* 3.6 28.7 - - + +
4A GLN 5.1 0.5 + - - -
5A PHE* 4.3 7.4 + - - +
155A PHE* 5.6 0.9 - - + +
156A PRO 3.7 7.6 - - - +
157A VAL* 4.1 16.3 - - + -
168A LYS 3.4 10.1 - - - +
169A VAL* 1.3 91.0 - - + +
171A VAL* 1.3 65.2 - - - +
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Residues in contact with VAL 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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3A PRO* 3.8 6.7 - - - -
5A PHE* 3.5 24.2 - - + +
7A VAL 4.1 0.7 - - - -
8A GLY* 3.7 28.7 - - - +
31A ALA* 5.3 1.3 - - + -
155A PHE* 3.4 4.7 - - - +
156A PRO* 3.1 27.8 + - - +
158A LEU* 4.6 7.9 - - + -
169A VAL* 4.0 15.7 - - + +
170A PRO* 1.3 81.3 - - - +
172A LYS* 1.3 61.3 + - - +
173A MET 3.4 19.5 - - - +
174A VAL* 3.7 23.6 - - + -
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Residues in contact with LYS 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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2A GLU* 3.2 28.7 - - - +
3A PRO* 2.9 32.7 + - + -
4A GLN 4.1 5.5 + - - -
5A PHE 3.2 8.3 + - - +
6A ASP* 2.7 38.7 + - - +
155A PHE* 3.6 20.9 - - + -
156A PRO* 3.6 5.3 - - - +
171A VAL* 1.3 75.5 - - - +
173A MET* 1.3 59.0 + - - +
308A ASN* 2.9 29.1 + - - +
345A HIS* 5.7 1.1 - - - +
350A TYR* 3.7 29.0 - - + +
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Residues in contact with MET 173 (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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6A ASP 2.9 11.8 + - - +
7A VAL* 3.1 18.5 - - + +
8A GLY 2.8 26.3 + - - -
171A VAL* 3.3 2.1 - - - +
172A LYS* 1.3 79.5 - - - +
174A VAL* 1.3 70.1 + - - +
175A VAL* 4.8 0.9 - - + -
308A ASN* 3.5 21.1 - - - -
309A PHE 3.5 27.4 - - - -
310A LEU* 3.6 9.4 - - + +
341A ILE* 3.3 33.7 - - + -
350A TYR* 3.9 18.2 - - + -
355A PHE* 3.3 26.7 - - + -
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Residues in contact with VAL 174 (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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8A GLY 3.5 6.3 - - - +
10A ILE* 4.2 11.2 - - + -
149A VAL* 4.1 11.4 - - + -
156A PRO* 3.6 28.7 - - + -
158A LEU* 3.9 27.8 - - + -
171A VAL* 3.7 16.4 - - + -
173A MET* 1.3 77.5 - - - +
175A VAL* 1.3 73.6 + - - +
176A ASP 4.3 1.3 - - - +
184A LEU* 4.4 10.1 - - + -
308A ASN 3.0 13.4 + - - +
309A PHE* 3.2 7.3 - - + -
310A LEU 3.0 24.3 + - - +
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Residues in contact with VAL 175 (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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7A VAL* 3.9 19.1 - - + -
8A GLY 2.9 7.5 + - - +
9A ILE* 3.4 16.3 - - + +
10A ILE* 2.9 26.9 + - - +
19A THR* 4.2 24.2 - - + +
173A MET* 4.1 6.7 + - + -
174A VAL* 1.3 78.4 - - - +
176A ASP* 1.3 61.9 + - - +
177A ALA 3.5 0.5 + - - -
310A LEU* 3.4 24.9 - - + -
312A VAL* 3.7 27.8 - - + -
341A ILE* 4.9 8.1 - - + -
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Residues in contact with ASP 176 (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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10A ILE* 4.1 11.7 - - + +
174A VAL* 4.1 1.6 - - - +
175A VAL* 1.3 69.5 - - - +
177A ALA* 1.3 58.7 + - - +
178A SER* 2.6 34.0 + - - -
182A THR* 4.1 0.5 - - - -
183A GLN* 3.6 4.5 + - - +
184A LEU* 2.9 45.9 + - + +
185A GLY 3.9 1.4 + - - -
310A LEU 2.8 10.5 + - - +
311A MET* 3.3 22.8 - - + +
312A VAL 2.9 27.9 + - - -
315A ALA* 3.5 10.9 - - - +
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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