Contacts of the strand formed by residues 133 - 137 (chain B) in PDB entry 1P4A
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 3.5 7.3 - - - +
132B ASP* 1.3 86.7 - - + +
134B VAL* 1.3 74.1 + - - +
135B MET* 4.4 0.9 - - + +
154B VAL* 4.1 1.3 - - - -
155B PRO* 3.6 23.1 - - + +
157B VAL* 3.8 30.7 - - + -
192B SER 5.5 1.1 - - - +
193B MET* 4.5 13.7 - - + -
197B SER* 5.2 1.8 - - - +
198B ASN 3.4 1.7 + - - +
199B VAL* 3.5 26.2 - - + -
200B LEU 3.0 23.4 + - - -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 4.8 1.1 - - + -
133B VAL* 1.3 75.0 - - - +
135B MET* 1.3 63.0 + - - +
145B ALA* 3.5 37.2 - - + +
148B ALA 4.6 0.4 - - - -
149B ALA* 3.9 19.1 - - + +
152B LEU* 4.6 4.3 - - + -
154B VAL* 3.7 20.4 - - + -
155B PRO 2.9 11.4 + - - +
156B VAL* 3.3 4.2 - - + +
157B VAL* 2.8 26.3 + - - +
200B LEU* 3.3 24.5 - - + +
202B ILE* 3.8 20.6 - - + -
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Residues in contact with MET 135 (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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133B VAL* 4.1 0.4 - - + -
134B VAL* 1.3 78.0 - - - +
136B THR* 1.3 63.5 + - - +
145B ALA* 4.8 0.4 - - - -
157B VAL* 3.3 16.8 - - + +
159B VAL* 3.8 22.9 - - + -
188B LEU* 3.6 30.5 - - + -
193B MET* 4.5 6.5 - - - -
199B VAL* 3.6 16.6 - - + -
200B LEU 2.8 10.1 + - - +
201B ILE* 3.4 7.5 - - + +
202B ILE* 2.9 25.5 + - - -
215B MET* 4.0 22.4 - - - +
218B LEU* 4.8 3.6 - - + -
219B LEU* 3.6 37.5 - - + -
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Residues in contact with THR 136 (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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135B MET* 1.3 73.2 - - - +
137B VAL* 1.3 68.3 + - - +
141B GLY* 3.5 7.3 - - - -
142B ILE* 3.8 28.3 - - + +
145B ALA* 3.7 24.0 - - + +
156B VAL* 5.2 0.2 - - + -
157B VAL 3.2 8.1 + - - +
158B ILE* 4.7 5.8 - - + -
159B VAL* 2.8 27.4 + - - +
202B ILE 2.8 24.1 + - - -
203B ASP* 3.5 13.5 + - - -
215B MET* 3.8 11.4 - - - -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 1.3 90.0 + - - +
138B ALA* 1.3 78.8 + - - +
139B THR* 3.5 3.1 + - - -
141B GLY 4.1 7.8 + - - -
159B VAL* 3.5 28.3 - - + +
160B ARG 5.0 0.4 - - - +
161B LYS* 3.9 18.6 - - + -
175B TYR* 4.8 6.5 - - - +
186B MET* 4.8 7.2 - - + -
203B ASP* 3.9 6.3 - - - +
211B THR* 3.6 28.0 - - + -
215B MET* 3.9 10.9 - - + -
605B PCP 3.7 17.5 + - - +
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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