Contacts of the strand formed by residues 133 - 138 (chain B) in PDB entry 1UZL
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLU 3.5 9.4 - - - -
127B MET* 3.7 17.9 - - - -
132B PHE* 1.3 79.8 - - - +
134B ARG* 1.3 82.1 + - - -
135B MET 4.1 0.9 - - - -
175B ASN 3.1 7.0 + - - -
176B VAL* 3.9 8.0 - - - +
177B THR 3.0 16.0 + - - -
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Residues in contact with ARG 134 (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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83B GLU 3.0 6.9 + - - +
84B VAL* 3.5 20.0 - - + +
85B LEU* 3.0 28.6 + - - +
127B MET* 4.1 0.8 - - - +
132B PHE* 3.5 37.8 - - + -
133B GLY* 1.3 81.8 + - - +
135B MET* 1.3 62.9 + - - +
136B ILE* 3.8 5.1 + - + -
175B ASN* 2.7 51.3 + - - +
177B THR* 3.3 23.6 + - - +
179B ASN* 6.1 0.7 - - - +
224B LEU 4.3 21.5 - - - +
225B ALA* 5.1 3.8 - - - -
226B SER 4.8 8.5 + - - -
227B GLU* 5.6 1.8 + - - +
229B ALA* 5.1 2.8 + - - -
230B SER* 3.7 34.4 - - - +
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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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85B LEU* 3.6 17.9 - - + +
120B ALA* 3.5 44.6 - - - +
123B ALA* 4.6 0.9 - - + -
124B SER* 4.0 17.0 - - - -
127B MET* 3.7 26.7 - - - -
134B ARG* 1.3 75.1 - - - +
136B ILE* 1.3 61.6 + - - +
137B PHE* 3.8 19.3 - - + -
167B ILE* 4.1 22.7 - - + -
171B LEU* 4.6 0.7 - - + -
176B VAL* 4.2 12.8 - - + -
177B THR* 2.9 14.4 + - - +
178B ALA* 3.3 3.9 - - + -
179B ASN* 3.0 28.0 + - - +
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Residues in contact with ILE 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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84B VAL* 4.1 24.0 - - + -
85B LEU 2.8 11.0 + - - +
86B VAL* 3.3 9.4 - - + +
87B SER 3.0 23.4 + - - -
134B ARG* 4.5 5.2 - - + +
135B MET* 1.3 77.3 - - - +
137B PHE* 1.3 63.6 + - - +
138B ILE* 4.1 10.5 - - + -
179B ASN* 3.5 7.6 - - + +
181B VAL* 3.9 27.1 - - + -
221B VAL* 4.1 19.5 - - + +
224B LEU* 3.8 23.6 - - + +
225B ALA* 3.8 28.3 - - + +
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Residues in contact with PHE 137 (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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85B LEU* 5.3 1.8 - - + -
87B SER* 3.5 26.2 - - - +
116B ALA* 3.9 22.0 - - + -
119B VAL* 5.2 0.7 - - + -
120B ALA* 4.0 15.7 - - + -
135B MET* 3.8 27.1 - - + -
136B ILE* 1.3 73.0 - - - +
138B ILE* 1.3 64.7 + - - +
139B GLY 3.7 0.4 + - - -
160B VAL* 3.6 24.7 - - + -
163B MET* 3.5 28.3 - - + -
164B ALA* 4.1 24.5 - - + -
167B ILE* 4.3 2.2 - - + -
178B ALA* 4.2 7.4 - - + -
179B ASN 3.0 18.7 + - - +
180B VAL* 3.4 6.4 - - + +
181B VAL 2.9 25.6 + - - +
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Residues in contact with ILE 138 (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 ILE* 4.3 16.4 - - + -
31B ILE* 3.9 3.1 - - + -
86B VAL* 3.8 17.9 - - + -
87B SER 2.8 18.4 + - - +
88B ASN* 3.5 26.9 - - - +
89B ALA* 3.2 11.0 - - + +
136B ILE* 4.1 5.2 - - + -
137B PHE* 1.3 77.9 - - - +
139B GLY* 1.3 79.3 + - - +
157B LYS* 3.0 14.6 + - - -
160B VAL* 6.1 1.3 - - - -
181B VAL* 3.7 12.8 - - + +
183B PRO* 4.1 13.7 - - + -
217B VAL* 4.7 2.2 - - + -
221B VAL* 3.6 30.5 - - + -
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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