Contacts of the strand formed by residues 138 - 143 (chain B) in PDB entry 1UMZ
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 MET 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 3.7 10.4 - - + +
134B TRP* 3.7 1.4 - - - -
135B ASN* 3.0 38.9 + - - +
137B TYR* 1.3 81.7 - - + +
139B ILE* 1.3 63.6 + - - +
140B VAL* 3.7 28.5 - - + -
150B VAL* 3.8 19.3 - - + -
151B PHE 3.4 11.7 - - - +
152B LYS* 4.2 7.6 - - + -
161B PHE* 3.7 5.3 - - - -
229B PHE* 3.4 25.1 - - + +
230B GLN 4.3 2.5 - - - +
231B ASP* 3.6 37.0 - - - +
232B LEU* 3.9 10.8 - - + +
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Residues in contact with ILE 139 (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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86B ILE* 3.6 36.8 - - + -
105B VAL* 4.9 3.1 - - + -
132B VAL* 4.3 6.3 - - + -
133B LEU 3.2 6.5 - - - +
134B TRP* 3.6 24.9 - - + -
138B MET* 1.3 73.2 - - - +
140B VAL* 1.3 63.2 + - - +
141B PHE* 3.7 26.7 + - + -
149B ARG 4.0 0.3 - - - +
150B VAL* 3.3 4.9 - - - +
151B PHE* 2.8 44.5 + - + +
161B PHE* 3.9 9.2 - - + -
162B PRO* 3.6 32.5 - - + -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B SER 3.7 0.2 - - - +
132B VAL* 3.3 8.3 - - - +
133B LEU* 2.8 44.8 + - + +
138B MET* 3.7 37.7 - - + -
139B ILE* 1.3 77.1 - - - +
141B PHE* 1.3 67.8 + - - +
142B LEU* 3.9 26.2 - - + +
147B PRO* 4.0 15.0 - - + -
149B ARG 3.5 10.3 - - - +
150B VAL* 4.2 3.4 - - + -
232B LEU* 4.0 16.4 - - + -
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Residues in contact with PHE 141 (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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86B ILE* 3.5 28.9 - - + -
87B ASP 3.4 22.7 - - - -
88B PHE* 3.9 18.6 - + + -
103B THR* 3.5 19.1 - - + -
104B ASN 3.8 4.0 - - - -
105B VAL* 3.7 23.1 - - + -
131B SER 3.5 5.4 - - - -
132B VAL* 4.8 1.1 - - + +
139B ILE* 3.7 19.1 - - + -
140B VAL* 1.3 76.4 - - - +
142B LEU* 1.3 60.6 + - - +
147B PRO* 3.3 5.0 - - - +
148B ILE* 2.8 44.2 + - + -
149B ARG* 3.0 42.6 + - + +
151B PHE* 5.0 2.2 - - + -
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Residues in contact with LEU 142 (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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55B HIS* 5.5 4.0 - - + +
88B PHE* 3.7 5.2 - - - -
130B TYR* 3.4 4.7 - - - -
131B SER* 2.8 56.9 + - - +
132B VAL 5.0 0.2 - - - -
133B LEU* 4.5 11.4 - - + +
140B VAL* 3.9 28.9 - - + +
141B PHE* 1.3 75.8 - - - +
143B VAL* 1.3 63.5 + - - +
144B ASP 3.8 9.4 - - - +
145B ASP* 4.0 15.7 - - - +
146B VAL 3.2 4.7 - - - +
147B PRO* 4.0 25.6 - - + -
148B ILE 4.5 0.2 - - - +
232B LEU* 6.1 0.2 - - + -
236B GLN* 5.2 7.4 - - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 4.7 0.7 - - + -
101B LEU* 3.8 26.2 - - + -
119B LEU* 4.2 3.1 - - + -
120B TRP* 3.6 27.5 - - + -
121B PHE* 3.7 28.9 - - + -
128B HIS* 5.1 0.2 - - + -
129B TYR 3.4 4.0 - - - +
130B TYR* 3.8 15.5 - - + -
142B LEU* 1.3 74.1 - - - +
144B ASP* 1.3 74.2 + - - +
145B ASP 3.1 0.5 + - - -
146B VAL* 2.8 25.4 + - - +
148B ILE* 3.7 23.1 - - + +
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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