Contacts of the strand formed by residues 154 - 158 (chain R) in PDB entry 3H1J
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 154 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99R ARG* 2.6 32.0 + - - -
105R GLU* 4.1 3.9 - - - +
108R GLN* 6.0 2.0 - - - -
149R ASN* 5.4 3.4 - - - -
150R SER 5.2 3.6 - - - -
151R GLY 4.9 3.2 + - - -
152R ASP* 3.7 2.2 - - - +
153R PHE* 1.3 75.0 - - - +
155R GLY* 1.3 53.9 + - - +
167R ALA* 3.7 9.8 - - - +
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Residues in contact with GLY 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R ARG* 3.1 13.4 + - - -
149R ASN* 2.9 26.0 + - - -
150R SER 4.0 5.3 + - - -
153R PHE 2.6 8.7 + - - -
154R GLY* 1.3 74.7 - - - +
156R TYR* 1.3 67.0 + - - +
165R TYR 3.1 1.3 + - - -
166R ASP 3.1 27.8 - - - -
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Residues in contact with TYR 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86R ASN* 3.5 16.7 + - - -
97R PHE* 3.5 32.4 - + - +
99R ARG* 3.7 29.0 - - - +
133R VAL* 4.5 1.9 - - - +
135R LEU* 3.4 18.1 - - + +
146R PRO* 3.7 17.7 - - + -
147R ILE 3.0 9.6 - - - +
148R ALA* 3.3 36.6 - - + -
150R SER 3.2 11.5 + - - +
151R GLY* 4.6 0.3 - - - -
155R GLY* 1.3 73.9 - - - -
157R TYR* 1.3 59.8 + - - +
163R SER 4.5 0.2 - - - -
164R HIS* 3.7 3.6 - - - +
165R TYR* 2.9 36.7 + - + +
166R ASP 3.6 15.3 - - - -
167R ALA 5.1 2.2 - - - -
169R GLY* 4.3 11.7 - - - -
180R LEU* 4.1 14.1 - - + -
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Residues in contact with TYR 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C PRO 5.9 0.2 - - - -
343C PRO* 5.8 0.9 - - - +
344C VAL* 3.7 27.3 + - - +
345C GLU* 5.5 1.1 - - + +
146R PRO* 4.2 2.0 - - - -
147R ILE* 2.6 45.7 + - + +
150R SER* 2.9 31.2 - - - +
151R GLY* 4.0 2.9 - - - -
156R TYR* 1.3 75.0 - - - +
158R CYS* 1.3 63.4 + - - +
159R PRO* 3.4 18.1 - - + +
162R GLY* 3.4 34.8 + - - -
163R SER 3.5 8.5 - - - -
164R HIS* 3.4 35.9 - + - -
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Residues in contact with CYS 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139R CYS* 3.5 17.3 - - + -
144R CYS* 3.4 32.8 - - - -
145R VAL 4.8 1.1 - - - -
146R PRO* 4.2 7.1 - - + +
157R TYR* 1.3 75.1 - - - +
159R PRO* 1.3 61.0 - - - +
160R CYS 3.1 5.1 + - - -
162R GLY* 3.2 27.4 + - - -
163R SER* 3.0 15.0 + - - +
165R TYR* 4.6 2.7 - - + -
501R FES 2.2 40.8 - - - -
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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