Contacts of the strand formed by residues 169 - 176 (chain S) in PDB entry 2A1T
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 169 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203R LYS 3.4 9.6 - - - -
204R LEU* 4.1 2.9 - - - +
205R THR 4.7 2.7 - - - -
165S ALA* 3.8 3.6 - - - +
166S ILE* 2.7 38.9 + - - +
167S ASP 3.4 0.4 + - - -
168S GLY* 1.3 79.5 - - - +
170S LEU* 1.3 64.4 + - - +
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Residues in contact with LEU 170 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202R GLN* 3.6 4.6 - - - -
203R LYS* 2.9 47.4 + - + +
204R LEU* 4.8 0.2 - - - +
151S SER* 3.2 29.4 - - - +
163S GLU* 3.5 31.2 - - + +
164S ARG 3.3 17.9 - - - +
165S ALA* 3.9 10.1 - - + -
166S ILE* 4.5 1.6 - - - -
169S GLY* 1.3 73.5 - - - -
171S GLU* 1.3 60.8 + - - +
172S THR* 4.1 2.4 + - - -
186S ARG* 6.0 3.1 - - + -
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Residues in contact with GLU 171 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R GLY* 4.5 11.8 - - - +
88R LEU* 4.7 2.3 - - - +
199R TRP* 3.4 23.2 + - - +
201R ASP 3.5 12.3 - - - +
202R GLN* 3.9 16.5 + - + -
163S GLU* 3.7 2.0 - - - +
164S ARG* 2.9 71.2 + - - +
166S ILE* 3.9 21.2 - - + +
170S LEU* 1.3 73.0 - - - +
172S THR* 1.3 61.6 + - - +
173S LEU* 3.5 16.2 - - + +
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Residues in contact with THR 172 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199R TRP* 4.1 1.2 - - - -
200R LEU* 3.0 29.4 + - + -
201R ASP* 3.1 36.2 + - - +
161S LYS* 3.6 33.8 + - + +
162S VAL 3.6 11.2 - - - +
163S GLU* 4.3 15.5 + - + +
170S LEU* 4.7 2.4 + - - +
171S GLU* 1.3 74.5 + - - +
173S LEU* 1.3 76.7 + - - +
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Residues in contact with LEU 173 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88R LEU* 3.7 29.8 - - + -
89R PRO* 6.2 1.3 - - + -
90R GLU* 5.9 0.7 - - - +
197R SER* 5.2 1.1 - - - -
198R GLU 3.6 4.5 - - - +
199R TRP* 3.8 12.8 - - + -
200R LEU* 3.9 5.8 - - - -
146S GLN 4.7 9.0 - - - +
147S GLY* 5.3 2.5 - - - -
161S LYS* 3.4 9.2 - - - +
162S VAL* 2.8 39.8 + - + +
164S ARG* 4.0 24.0 - - - +
171S GLU* 3.5 22.0 - - - +
172S THR* 1.3 84.6 - - - +
174S ARG* 1.3 58.8 + - - +
175S LEU* 3.9 25.1 - - + -
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Residues in contact with ARG 174 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196R ILE 4.3 0.2 - - - +
197R SER* 3.5 3.1 - - - -
198R GLU* 2.9 60.4 + - - +
200R LEU* 3.5 32.2 - - + +
156S GLU* 3.1 36.0 + - - +
159S LYS* 3.5 43.5 + - + +
160S LEU 3.3 16.2 - - - +
161S LYS* 4.3 3.6 - - - +
173S LEU* 1.3 73.2 - - - +
175S LEU* 1.3 62.3 + - - +
176S LYS 4.5 0.2 + - - -
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Residues in contact with LEU 175 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196R ILE 3.6 2.5 - - - -
197R SER* 3.7 22.0 - - - -
145S PRO* 4.1 11.0 - - + -
146S GLN 3.9 6.7 - - - +
147S GLY* 3.8 26.2 - - - +
159S LYS* 3.3 8.0 - - - -
160S LEU* 3.0 37.0 + - + +
162S VAL* 3.7 29.4 - - + -
173S LEU* 3.9 20.0 - - + -
174S ARG* 1.3 83.7 - - - +
176S LYS* 1.3 70.2 + - - +
177S LEU* 4.1 1.0 - - - -
179S ALA* 4.6 14.8 - - + -
180S VAL 4.9 0.4 - - - +
181S VAL* 4.9 0.9 - - + -
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Residues in contact with LYS 176 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195R GLU 3.1 28.1 + - - +
196R ILE* 2.8 34.6 + - + +
145S PRO* 3.1 12.7 - - + +
158S ASP 4.0 5.4 - - - +
159S LYS* 4.1 30.0 - - + +
174S ARG 4.5 0.2 + - - -
175S LEU* 1.3 71.7 - - - +
177S LEU* 1.3 59.7 + - - +
178S PRO* 3.1 19.8 - - + +
179S ALA* 3.9 2.1 - - - +
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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