Contacts of the strand formed by residues 169 - 177 (chain B) in PDB entry 4H1S
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 GLU 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B TRP* 3.5 48.0 - - + +
165B PRO* 3.4 5.4 - - - +
166B VAL 2.8 30.7 + - - +
167B GLY 4.2 1.2 - - - +
168B ASP* 1.3 91.8 - - + +
170B VAL* 1.3 67.5 + - - +
214B LYS* 3.4 26.3 + - - -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B VAL* 3.7 26.2 - - + -
164B LEU 3.1 11.7 - - - +
165B PRO* 4.1 10.5 - - + -
169B GLU* 1.3 82.3 + - - +
171B VAL* 1.3 67.2 + - - +
211B ASN 5.4 1.8 - - - +
212B VAL* 4.3 23.1 - - + +
213B ASN* 5.2 0.7 + - - +
214B LYS* 3.6 20.1 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 4.0 26.7 - - + -
29B LEU* 4.5 10.5 - - + -
79B LEU* 4.4 11.2 - - + -
162B LYS 3.8 0.7 - - - +
163B VAL* 4.6 1.3 - - - -
164B LEU* 2.8 36.7 + - + +
166B VAL* 4.3 10.5 - - + -
170B VAL* 1.3 79.9 - - - +
172B GLY* 1.3 72.1 + - - +
173B ILE* 3.9 2.2 + - + +
212B VAL* 4.3 2.0 - - - -
214B LYS* 3.4 24.5 - - + +
216B ILE* 3.8 28.9 - - + -
294B PHE* 6.0 0.7 - - + -
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS 3.6 6.3 - - - -
163B VAL* 4.5 3.8 - - - -
171B VAL* 1.3 74.7 - - - +
173B ILE* 1.3 59.3 + - - +
174B VAL 4.2 0.4 - - - -
207B LEU* 4.4 10.8 - - - -
212B VAL* 3.5 15.8 - - - +
214B LYS 2.8 14.1 + - - -
215B ILE* 3.4 8.6 - - - +
216B ILE 2.7 32.4 + - - +
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Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.5 8.3 - - + -
81B LEU* 3.7 23.1 - - + -
112B ALA* 4.0 5.6 - - + -
140B LEU* 3.6 22.1 - - + +
161B TYR* 3.1 3.7 - - - +
162B LYS 2.9 40.6 + - - +
164B LEU* 3.5 33.7 - - + -
171B VAL* 4.4 5.6 - - + +
172B GLY* 1.3 78.9 - - - +
174B VAL* 1.3 62.8 + - - +
207B LEU* 4.9 0.6 - - - +
216B ILE* 3.2 19.3 - - + +
218B LEU* 3.7 31.9 - - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ALA* 4.0 2.5 - - + -
160B PRO 3.3 17.0 - - - +
161B TYR* 4.1 1.8 - - + -
173B ILE* 1.3 76.5 - - - +
175B GLY* 1.3 59.7 + - - +
176B TYR* 4.4 1.2 - - - -
200B LEU* 3.5 26.9 - - + +
203B GLU* 3.7 22.4 - - + -
204B VAL* 4.1 18.4 - - + +
207B LEU* 3.5 31.2 - - + -
215B ILE* 4.1 10.5 - - + -
216B ILE 2.9 6.7 + - - +
217B ALA* 3.4 6.8 - - + +
218B LEU 2.8 25.3 + - - +
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 4.5 0.4 - - - -
140B LEU* 3.8 26.4 - - - +
141B SER* 3.6 3.1 - - - -
142B ALA* 2.7 34.6 + - - +
160B PRO 3.2 11.1 + - - -
174B VAL* 1.3 73.5 - - - +
176B TYR* 1.3 62.5 + - - +
200B LEU* 3.6 2.9 - - - +
218B LEU* 3.0 9.6 - - - -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 4.2 2.9 - - - +
115B LEU 3.7 4.2 - - - +
141B SER* 4.0 2.7 - - - +
143B ASN* 3.4 12.3 - - + +
175B GLY* 1.3 77.2 - - - +
177B THR* 1.3 64.8 + - - +
196B GLU* 4.1 10.8 - - + -
200B LEU* 4.0 23.3 - - + -
217B ALA* 3.9 10.5 - - + -
218B LEU 3.2 18.8 + - - -
219B GLY* 3.1 37.2 + - - -
220B HIS 2.9 22.3 + - - -
221B SER* 3.3 26.0 - - - -
226B ASP* 2.5 27.6 + - - -
229B ILE* 3.5 27.3 - - + +
239B VAL* 3.3 17.7 - - - +
240B VAL 3.9 1.4 + - - -
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 2.8 31.1 + - - +
116B GLY* 4.0 13.2 - - - +
117B ASN 4.3 0.2 - - - +
120B PHE* 4.5 1.3 - - + -
141B SER* 2.7 30.0 + - - -
143B ASN* 2.7 33.5 + - - -
144B ILE* 3.6 19.2 - - + +
176B TYR* 1.3 74.0 - - - +
178B SER* 1.3 68.3 + - - +
179B LYS 3.2 0.3 + - - -
181B THR* 3.7 17.5 - - - +
193B PHE* 4.1 3.5 - - + -
196B GLU* 3.8 2.0 - - - +
220B HIS 4.0 2.5 - - - -
221B SER* 3.6 3.8 - - - -
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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