Contacts of the strand formed by residues 174 - 179 (chain B) in PDB entry 4CY1
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 VAL 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE* 3.7 15.9 - - - +
134B CYS* 3.6 9.4 - - - -
147B GLY* 3.8 17.2 - - - -
148B SER 3.1 17.2 + - - +
151B GLU* 3.7 22.9 - - - +
152B SER 3.6 20.9 - - - +
153B VAL* 4.0 7.6 - - + -
170B HIS* 3.9 16.4 - - + -
172B ASP 4.2 0.9 - - - +
173B PRO* 1.3 72.7 - - - +
175B SER* 1.3 60.9 + - - +
176B ALA 3.8 15.5 - - - +
177B VAL* 4.0 7.4 - - + -
188B SER* 4.4 3.4 - - - -
189B SER 3.4 14.6 - - - +
190B SER* 4.3 0.4 - - - -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.3 24.8 - - - -
134B CYS* 3.7 6.1 - - - +
173B PRO 3.6 2.0 + - - -
174B VAL* 1.3 74.7 - - - +
176B ALA* 1.3 61.1 + - - +
189B SER* 2.8 24.2 + - - -
190B SER* 4.7 0.2 - - - -
191B TYR* 4.1 10.1 - - - -
217B VAL 2.6 26.6 + - - -
218B SER 3.5 20.7 - - - +
219B PHE* 5.2 0.2 - - - -
261B CYS* 3.8 14.6 - - - -
592C ARG* 4.0 5.7 + - - -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B CYS* 3.5 9.9 - - - -
174B VAL* 3.5 2.1 - - - +
175B SER* 1.3 82.7 + - - +
177B VAL* 1.3 69.2 + - - +
187B VAL 4.4 0.9 - - - -
188B SER* 3.3 1.6 - - - -
189B SER* 3.1 36.8 + - - +
219B PHE* 4.0 15.5 - - + -
220B VAL* 3.5 29.2 - - + +
592C ARG* 6.0 0.2 - - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B CYS* 3.7 26.4 - - - +
135B CYS* 4.0 2.9 + - - +
136B ASN* 2.8 20.6 + - - -
145B VAL* 3.7 40.8 - - + +
146B SER 3.9 9.6 - - - +
147B GLY 3.9 3.4 - - - +
153B VAL* 3.9 27.4 - - + -
174B VAL* 4.0 7.6 - - + -
176B ALA* 1.3 82.6 - - - +
178B HIS* 1.3 62.1 + - - +
186B ILE* 4.7 1.3 - - + -
187B VAL 3.3 7.2 - - - +
188B SER* 4.2 5.2 - - - -
220B VAL 5.1 0.2 - - - -
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASN* 3.5 24.9 - - - +
145B VAL* 4.4 1.2 - - - +
177B VAL* 1.3 75.8 - - - +
179B PHE* 1.3 86.2 + - - +
186B ILE* 3.3 5.4 - - - +
187B VAL* 2.9 42.5 + - + -
220B VAL 4.3 2.7 - - - +
221B LYS* 3.9 30.5 - - + -
222B PHE* 3.1 42.7 + - + -
223B SER 5.7 0.4 - - - -
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASN* 3.9 2.5 - - - +
137B PHE 3.4 7.9 - - - +
138B ASN* 3.4 49.6 - - + -
139B PRO* 4.0 3.4 - - + -
143B LEU* 4.3 14.6 - - + -
144B ILE 4.3 2.0 - - - -
145B VAL* 3.4 44.6 - - + -
155B ILE* 5.0 2.5 - - + -
178B HIS* 1.3 100.4 + - - +
180B ASN* 1.3 69.1 + - - +
183B GLY 3.7 15.9 - - - -
185B LEU 3.3 10.3 - - - -
186B ILE* 3.4 20.2 - - + -
200B THR* 3.6 19.1 - - + -
222B PHE* 3.6 2.0 - - - -
1335B GOL 4.5 0.2 - - - -
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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
------------------------------------------------------------
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