Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 4D85
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 SER 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY 3.5 7.2 - - - -
11A LYS* 4.6 3.8 - - - +
159A ALA* 3.4 23.9 - - - +
160A ALA* 1.3 83.0 + - - +
162A VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 162 (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 ARG* 3.6 10.4 - - - -
10A GLY* 2.7 56.2 + - - +
11A LYS 4.0 1.8 - - - +
12A SER* 3.6 33.7 - - - +
15A GLY 4.4 3.6 - - - +
16A TYR* 3.7 32.3 - - + +
157A CYS 4.1 3.4 - - - +
158A GLY* 4.7 1.3 - - - -
159A ALA* 3.7 19.5 - - - +
161A SER* 1.3 81.9 - - - +
163A GLY* 1.3 59.0 + - - +
326A GLU* 5.5 0.9 - - - +
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Residues in contact with GLY 163 (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* 4.7 1.8 - - - -
8A LEU 3.2 12.3 - - - -
9A ARG* 3.9 10.3 - - - -
16A TYR* 3.3 9.5 - - - -
157A CYS* 2.9 36.1 + - - +
159A ALA* 5.3 0.4 - - - +
162A VAL* 1.3 76.8 - - - +
164A GLY* 1.3 58.4 + - - -
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Residues in contact with GLY 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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6A ASP* 3.1 20.2 + - - -
8A LEU* 2.9 36.7 + - - +
16A TYR* 4.9 0.2 - - - -
155A GLN* 3.0 15.0 - - - -
156A LEU* 4.4 1.1 - - - -
157A CYS* 4.2 8.3 - - - -
163A GLY* 1.3 74.1 - - - -
165A SER* 1.3 62.1 + - - -
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Residues in contact with SER 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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5A VAL* 3.7 9.2 - - - +
6A ASP* 2.9 24.6 + - - +
7A ASN* 3.5 4.9 - - - -
8A LEU* 3.6 7.5 - - - +
153A SER 3.8 0.5 - - - +
154A LEU* 3.4 3.6 - - - -
155A GLN* 2.9 44.0 + - - -
164A GLY* 1.3 73.8 - - - -
166A MET* 1.3 60.0 + - - +
167A ILE* 3.9 11.4 - - - +
175A LEU* 3.9 24.0 - - - +
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Residues in contact with MET 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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4A MET* 3.7 4.3 - - - +
7A ASN* 2.8 33.3 + - - +
8A LEU* 3.8 5.8 - - + +
18A VAL* 3.8 22.9 - - + -
33A VAL* 3.3 32.5 - - + -
89A ILE* 5.7 1.6 - - + -
121A LEU* 5.0 8.5 - - + -
123A LEU* 4.2 19.7 - - - -
139A PHE* 6.3 0.9 - - - -
152A PHE* 4.9 8.3 - - + -
153A SER 3.4 6.7 - - - +
154A LEU* 3.6 22.4 - - + -
165A SER* 1.3 71.0 - - - +
167A ILE* 1.3 63.1 + - - +
168A ILE* 3.5 32.6 + - + +
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Residues in contact with ILE 167 (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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1A PHE* 3.6 41.1 - - + +
4A MET* 3.9 23.6 - - + -
5A VAL* 4.3 2.5 - - + +
152A PHE* 3.4 4.9 - - - +
153A SER* 3.0 39.0 + - - +
165A SER* 4.0 10.8 - - - -
166A MET* 1.3 74.7 - - - +
168A ILE* 1.3 61.4 + - - +
170A GLY* 3.5 19.6 - - - +
171A ILE 4.3 0.4 - - - +
172A ASP* 4.0 7.4 - - + +
175A LEU* 3.9 23.1 - - + -
329A TYR* 3.6 17.9 - - + +
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Residues in contact with ILE 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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1A PHE* 4.6 2.3 - - - -
4A MET* 3.3 29.8 - - + +
7A ASN* 5.8 0.7 - - - +
89A ILE* 3.3 37.5 - - + -
92A GLY* 5.6 0.4 - - - -
93A PRO* 4.2 18.2 - - + +
138A PHE* 5.6 0.7 - - + -
139A PHE* 3.8 16.8 - - + -
142A LEU* 3.7 27.6 - - + -
148A VAL* 4.2 9.1 - - + +
152A PHE* 4.3 4.7 - - + -
166A MET* 3.7 33.4 - - + +
167A ILE* 1.3 70.5 - - - +
169A GLY* 1.3 62.8 + - - +
170A GLY* 3.1 8.1 + - - -
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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