Contacts of the strand formed by residues 178 - 186 (chain B) in PDB entry 3S8W
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 ASN 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU* 4.0 31.8 + - + +
114A ILE 3.1 30.0 + - - +
115A VAL* 4.6 6.7 - - - +
124A MSE 4.9 3.8 - - - +
147B SER* 2.7 32.1 + - - -
177B THR* 1.3 75.0 - - - +
179B TYR* 1.3 71.8 + - - +
180B CYS* 6.0 0.2 - - - -
200B CYS* 4.4 3.3 - - - +
201B THR 3.1 19.0 + - - +
202B LEU* 3.8 13.3 - - + +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.8 20.2 - - + -
145B GLU* 4.2 17.9 - - + -
146B GLN 3.4 7.0 - - - +
147B SER* 3.8 20.9 - - - -
173B LEU* 3.4 31.3 - - + +
174B ILE* 2.9 30.0 + - - +
177B THR* 3.3 47.6 - - + +
178B ASN* 1.3 73.6 + - - +
180B CYS* 1.3 64.5 + - - +
181B VAL* 5.3 1.6 - - + -
199B LYS 3.9 0.5 - - - +
200B CYS* 3.1 3.8 - - - +
201B THR* 2.7 43.4 + - - +
203B LEU* 3.6 28.7 - - + -
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Residues in contact with CYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 4.3 8.3 - - - -
199A LYS* 3.9 23.6 - - - -
144B GLU 3.8 0.3 - - - +
145B GLU* 3.6 2.1 - - - -
146B GLN* 2.9 51.9 + - + +
178B ASN* 5.0 1.1 - - - -
179B TYR* 1.3 75.7 - - - +
181B VAL* 1.3 62.5 + - - +
198B LEU* 4.0 14.6 - - + -
199B LYS 3.3 3.6 - - - -
200B CYS* 2.1 44.2 - - - -
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.7 16.3 - - + -
114B ILE* 4.3 16.8 - - + -
121B ILE* 4.3 20.2 - - + -
123B VAL* 4.6 6.5 - - + -
143B ILE* 3.8 20.6 - - + -
144B GLU 3.0 11.2 - - - +
145B GLU* 4.8 2.7 - - + -
170B ILE* 4.0 20.6 - - + -
179B TYR* 5.3 0.9 - - + -
180B CYS* 1.3 79.4 - - - +
182B SER* 1.3 71.7 + - - +
183B VAL* 4.4 1.8 - - + -
198B LEU* 3.3 6.1 - - - -
199B LYS 2.7 43.0 + - - +
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Residues in contact with SER 182 (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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112B PHE* 4.4 0.4 - - - -
144B GLU* 2.6 55.0 + - - +
146B GLN* 5.4 0.2 - - - -
181B VAL* 1.3 75.0 - - - +
183B VAL* 1.3 66.7 + - - +
184B TYR* 4.1 5.5 - - - -
195B LYS* 3.8 11.6 - - - +
196B SER* 3.1 34.7 + - - -
198B LEU* 3.6 19.5 - - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PRO* 3.6 7.8 - - - +
110B PRO* 3.5 26.4 - - + +
112B PHE* 3.4 45.5 - - + -
123B VAL* 4.6 1.8 - - + -
125B VAL* 4.2 14.4 - - + -
141B LEU* 3.7 16.2 - - + -
142B VAL 3.4 3.8 - - - +
143B ILE* 4.5 12.1 - - + -
181B VAL* 4.4 5.6 - - + -
182B SER* 1.3 79.8 + - - +
184B TYR* 1.3 66.9 + - - +
196B SER* 2.9 25.5 + - - -
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Residues in contact with TYR 184 (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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109B PRO* 4.6 1.8 - - + -
110B PRO* 4.1 7.2 - - - -
141B LEU* 3.3 9.2 - - - +
142B VAL* 2.9 61.1 + - + +
144B GLU* 2.8 32.8 + - + -
153B LYS* 3.4 20.1 + - - +
182B SER* 4.1 6.5 - - - -
183B VAL* 1.3 80.4 - - - +
185B LEU* 1.3 67.5 + - - +
186B GLU* 4.3 8.5 - - - -
193B VAL* 4.1 30.1 - - + -
194B ILE 3.4 22.4 - - - +
195B LYS* 3.4 36.0 + - + -
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Residues in contact with LEU 185 (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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107B PHE* 4.3 39.7 + - + +
108B GLU 3.8 20.6 - - - +
109B PRO* 5.3 1.0 - - - +
110B PRO* 4.1 16.4 - - + +
127B PHE* 4.8 14.4 - - + -
139B LEU* 4.9 15.5 - - + +
140B SER 3.5 16.8 - - - +
141B LEU* 3.9 17.0 - - + +
184B TYR* 1.3 86.8 - - - +
186B GLU* 1.3 60.0 + - - +
193B VAL* 4.2 12.5 - - - +
194B ILE 5.0 1.3 + - - -
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Residues in contact with GLU 186 (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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139B LEU* 3.4 4.2 - - - -
140B SER* 2.7 47.3 + - - +
142B VAL* 3.5 25.5 - - + +
153B LYS* 2.9 26.1 + - - -
155B LYS* 3.0 27.4 + - - +
184B TYR* 4.3 5.3 - - + -
185B LEU* 1.3 74.4 - - - +
187B HIS* 1.3 59.5 + - - +
188B SER* 3.4 29.9 + - - +
189B ASP* 4.3 2.4 + - - +
193B VAL* 3.7 18.3 - - + +
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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