Contacts of the strand formed by residues 162 - 168 (chain A) in PDB entry 3S5D
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 GLY 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 4.0 1.0 - - - +
157A SER* 3.9 2.0 - - - -
158A SER* 2.9 40.3 + - - -
160A SER 3.6 1.8 + - - -
161A SER* 1.3 80.0 - - - +
163A PRO* 1.3 73.5 - - - +
164A LYS* 3.8 4.2 + - - +
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Residues in contact with PRO 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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156A LEU 3.3 9.9 - - - +
157A SER* 4.5 6.1 - - - +
161A SER 4.6 1.1 - - - +
162A GLY* 1.3 84.8 - - - +
164A LYS* 1.3 66.5 + - - +
165A ARG* 5.9 0.9 - - + -
175A TYR* 4.5 5.4 + - - -
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Residues in contact with LYS 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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156A LEU* 2.8 39.3 + - + +
161A SER* 3.0 43.6 + - - +
162A GLY 3.8 3.5 + - - +
163A PRO* 1.3 80.3 - - - +
165A ARG* 1.3 64.8 + - - +
166A TYR* 3.7 18.0 - - + +
175A TYR* 3.8 40.8 - - + +
178A ASP* 4.3 12.1 + - - -
185A LEU* 3.7 33.9 - - + +
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Residues in contact with ARG 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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148A GLN* 5.0 9.9 - - - -
151A ASN* 4.0 11.6 - - - +
153A GLN* 3.0 39.1 + - + +
154A ILE 3.5 5.6 - - - +
155A ALA* 4.3 19.1 - - + -
163A PRO* 6.4 0.4 - - + -
164A LYS* 1.3 79.5 - - - +
166A TYR* 1.3 63.3 + - - +
167A ASP* 4.2 2.3 + - - +
174A VAL 4.0 0.5 - - - +
175A TYR* 3.4 27.3 - - - -
176A SER* 4.4 2.1 + - - -
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Residues in contact with TYR 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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153A GLN* 3.2 9.6 - - - -
154A ILE* 2.8 45.1 + - + +
156A LEU* 3.5 18.4 - - + +
164A LYS* 3.7 26.3 - - + +
165A ARG* 1.3 77.0 - - - +
167A ASP* 1.3 63.6 + - - +
173A TRP* 3.5 28.6 - - + -
174A VAL 3.4 4.5 - - - +
175A TYR* 3.3 34.9 - - + +
180A VAL 3.6 6.4 + - - -
181A SER 3.8 0.2 - - - -
182A LEU* 3.3 37.9 - - + -
185A LEU* 3.1 34.3 - - - +
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Residues in contact with ASP 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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152A LYS 5.0 1.1 - - - -
153A GLN* 2.9 33.7 + - - +
165A ARG 4.9 1.6 - - - +
166A TYR* 1.3 74.3 - - - +
168A TRP* 1.3 68.1 + - - +
169A THR* 3.5 4.9 + - + +
173A TRP* 3.3 6.4 - - - -
174A VAL 3.0 34.6 + - - +
176A SER* 4.1 19.8 + - - -
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Residues in contact with TRP 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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90A LEU* 3.7 42.3 - - + +
98A LEU* 3.5 36.5 - - + +
152A LYS 4.7 3.7 + - - +
167A ASP* 1.3 77.3 - - - +
169A THR* 1.3 58.1 + - - +
170A GLY* 3.2 43.3 + - - -
171A LYS* 3.4 17.9 - - - -
172A ASN* 3.3 33.4 - - - -
173A TRP* 3.6 42.9 - + + -
205A TYR* 3.8 15.7 - + + -
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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