Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 1D02
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 PHE 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.9 4.3 - - - +
96B PHE 3.2 11.9 - - - +
122B SER 5.4 0.2 - - - -
125B LEU* 3.4 61.0 - - + -
126B PHE* 3.8 18.2 - + - -
131B LEU* 4.0 5.6 - - + -
134B TYR* 3.9 13.5 - + + -
146B LEU* 3.2 35.8 + - + +
147B PRO* 1.3 87.9 - - + +
149B TRP* 1.3 64.6 + - - +
150B VAL* 3.8 9.0 - - + -
170B TYR* 3.7 28.7 - + - -
176B ASN* 2.8 26.4 + - + +
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Residues in contact with TRP 149 (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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31B PHE* 3.7 24.9 - + - -
84B PHE* 3.8 25.0 - + + -
86B ILE* 4.3 6.1 - - + -
95B LEU* 4.0 22.9 - - + -
96B PHE 3.0 7.0 + - - +
97B GLY* 3.2 4.2 - - - -
98B GLU 3.0 22.9 + - - +
148B PHE* 1.3 76.6 - - - +
150B VAL* 1.3 68.2 + - - +
151B VAL* 3.8 11.6 + - + -
175B ASP 4.1 0.2 - - - -
176B ASN* 3.4 18.4 - - - -
177B TYR* 3.8 1.8 - - - -
178B PHE* 3.5 29.1 - - + +
189B LEU* 3.7 35.4 - - + -
192B HIS* 3.6 23.1 + - - -
193B PHE* 3.9 13.0 - - + -
197B LEU* 3.5 20.6 - - + -
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Residues in contact with VAL 150 (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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98B GLU* 3.6 12.1 - - + +
100B LYS* 4.3 9.6 - - + -
122B SER* 4.3 18.8 - - - +
125B LEU* 4.0 14.1 - - + -
148B PHE* 3.8 19.3 - - + -
149B TRP* 1.3 73.3 - - - +
151B VAL* 1.3 65.8 + - - +
152B PHE* 3.6 32.8 + - + -
170B TYR* 3.3 24.7 - - - +
176B ASN 3.1 7.4 + - - +
177B TYR* 3.1 5.0 - - - +
178B PHE 2.9 24.1 + - - +
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Residues in contact with VAL 151 (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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27B LEU* 3.9 24.7 - - + -
84B PHE* 4.2 6.7 - - + -
98B GLU 2.9 13.4 + - - +
99B ILE* 3.2 7.1 - - + +
100B LYS 2.8 24.4 + - - -
149B TRP* 3.8 35.2 - - + +
150B VAL* 1.3 76.3 - - - +
152B PHE* 1.3 71.1 + - - +
153B GLU* 4.3 13.2 - - - +
178B PHE* 3.4 9.0 - - + +
180B TRP* 4.1 16.6 - - + -
189B LEU* 4.1 11.9 - - + -
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Residues in contact with PHE 152 (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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100B LYS* 3.2 34.1 - - + +
119B HIS* 4.3 13.5 - + + -
122B SER* 4.3 8.7 - - - -
150B VAL* 3.6 24.5 - - + -
151B VAL* 1.3 74.4 - - - +
153B GLU* 1.3 65.1 + - - +
156B ILE* 4.5 13.9 - - + -
157B THR* 3.6 4.7 - - + -
166B ILE* 3.7 45.8 - - + -
169B TRP* 5.1 2.5 - + - -
170B TYR* 4.7 6.3 - + - -
177B TYR* 3.8 13.9 - + + -
178B PHE 2.9 14.1 + - - +
179B MET* 3.9 30.1 - - + -
180B TRP* 2.9 27.7 + - - +
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Residues in contact with GLU 153 (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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27B LEU* 4.6 3.8 + - - +
99B ILE* 3.7 27.0 - - + +
100B LYS 2.9 4.4 + - - -
101B ARG* 3.3 37.2 + - + +
102B GLN 3.1 22.3 + - - -
151B VAL* 4.3 6.9 - - + +
152B PHE* 1.3 80.2 - - - +
154B GLY* 1.3 63.7 + - - +
156B ILE* 3.3 7.4 - - - +
157B THR* 3.8 2.5 - - - -
180B TRP* 3.4 45.3 - - + +
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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