Contacts of the strand formed by residues 172 - 182 (chain A) in PDB entry 1UHG
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 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A VAL* 6.2 0.4 - - + -
105A LEU* 3.8 33.4 - - + -
106A TYR 3.0 22.9 - - - +
107A ALA* 3.9 17.0 - - - -
129A LEU* 4.8 2.5 - - - -
134A PHE* 4.4 0.9 - - - -
170A THR* 4.3 0.2 - - - +
171A ALA* 1.3 82.2 - - - +
173A VAL* 1.3 63.2 + - - +
312A LEU* 3.6 31.0 - - + -
315A ILE* 4.4 10.8 - - + -
321A LEU* 3.8 23.8 - - + -
322A LYS 3.3 10.4 + - - +
323A ILE* 3.5 15.6 - - + -
324A SER* 2.8 31.6 + - - -
325A GLN 3.7 0.5 + - - -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 3.5 1.6 - - - +
105A LEU* 3.3 6.4 - - - -
106A TYR* 2.7 46.6 + - + +
134A PHE* 3.8 13.7 - - + -
145A ILE* 4.7 2.5 - - + -
161A LEU* 4.0 30.3 - - + -
166A VAL* 4.2 12.8 - - + -
170A THR* 3.6 24.9 - - + -
172A MET* 1.3 78.1 - - - +
174A LEU* 1.3 63.9 + - - +
175A VAL* 4.0 14.5 + - + -
325A GLN* 3.5 20.0 - - + +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 4.0 36.3 - - + +
38A LEU* 5.0 10.3 - - + -
40A MET* 4.9 2.7 - - + -
41A VAL* 4.5 14.8 - - + -
103A SER* 4.8 0.7 - - - +
104A ARG 3.5 18.4 - - - +
105A LEU* 4.0 23.8 - - + -
172A MET 4.4 0.2 + - - -
173A VAL* 1.3 75.9 - - - +
175A VAL* 1.3 66.9 + - - +
176A ASN* 5.2 2.2 - - + -
293A LEU* 5.0 8.1 - - + -
297A LEU* 6.2 1.6 - - + -
323A ILE* 4.6 10.7 - - + +
325A GLN 3.0 13.0 + - - +
326A ALA* 3.3 18.5 - - + -
327A VAL* 3.0 27.9 + - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 4.0 1.1 - - - -
103A SER* 3.2 2.6 + - - -
104A ARG* 2.9 47.3 + - + +
106A TYR* 4.0 19.7 - - + -
145A ILE* 3.7 24.2 - - + -
148A TRP* 4.2 11.7 - - + -
149A VAL* 4.2 14.8 - - + -
160A VAL* 4.5 4.9 - - + -
161A LEU* 4.3 5.2 - - + -
173A VAL* 4.0 13.2 - - + -
174A LEU* 1.3 79.6 - - - +
176A ASN* 1.3 61.9 + - - +
327A VAL* 3.8 17.9 - - + -
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Residues in contact with ASN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.3 33.7 + - - +
34A ILE* 3.6 4.4 + - - +
37A ALA* 3.7 12.8 - - + +
101A LEU* 4.0 7.7 - - - +
102A ALA 3.5 2.7 - - - -
103A SER* 2.9 29.6 + - - +
160A VAL* 6.0 1.3 - - - +
174A LEU* 5.2 2.0 - - + -
175A VAL* 1.3 74.7 - - - +
177A ALA* 1.3 59.6 + - - +
293A LEU* 4.9 6.3 - - + -
327A VAL* 3.0 14.0 + - - +
328A HIS* 2.9 35.1 + - - +
329A ALA 3.1 21.3 + - - -
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER 3.8 0.3 - - - +
101A LEU* 3.5 6.0 - - - +
102A ALA* 2.9 38.5 + - + +
149A VAL* 3.8 27.1 - - + -
153A THR* 4.4 4.8 - - + +
157A ILE* 3.7 23.3 - - + -
160A VAL* 5.2 2.7 - - + -
176A ASN* 1.3 76.8 - - - +
178A ILE* 1.3 62.2 + - - +
329A ALA* 3.2 9.4 - - + +
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A CYS* 3.6 20.4 - - + -
33A ALA* 4.8 0.7 - - + -
99A PHE* 3.2 55.4 - - + -
100A SER 2.8 30.1 - - - +
101A LEU* 3.9 10.8 - - + +
153A THR* 5.3 0.2 - - - -
157A ILE* 3.5 5.0 - - - +
177A ALA* 1.3 74.9 - - - +
179A VAL* 1.3 66.5 + - - +
328A HIS* 4.6 4.7 - - + -
329A ALA 2.9 5.2 + - - +
330A ALA* 3.4 26.9 - - + -
331A HIS 2.9 25.7 + - - -
378A PHE* 3.7 12.8 - - + -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A SER 3.7 1.1 - - - +
99A PHE* 3.4 4.0 - - - -
100A SER* 2.9 41.0 + - - +
153A THR* 3.6 37.5 - - + +
154A ASN* 5.6 0.7 - - - +
156A ILE* 3.6 30.3 - - + -
157A ILE* 3.7 9.2 - - + -
178A ILE* 1.3 81.4 - - - +
180A PHE* 1.3 64.6 + - - +
331A HIS* 3.3 18.2 - - + -
154B ASN* 3.9 16.8 - - - +
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.9 20.9 - + + -
98A SER 3.3 11.2 - - - -
99A PHE* 4.2 15.3 - + + -
179A VAL* 1.3 79.6 - - - +
181A LYS* 1.3 67.3 + - - +
182A GLY* 3.8 22.0 - - - -
234A PHE* 3.8 31.6 - + - -
239A MET* 3.8 30.3 - - + -
331A HIS* 3.0 7.6 + - - -
332A ALA* 3.4 31.9 - - + +
333A GLU 3.7 4.4 + - - +
334A ILE* 5.3 4.5 - - + -
368A ILE* 3.8 21.3 - - + -
378A PHE* 3.5 28.0 - + + -
154B ASN* 5.1 0.2 - - - -
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.3 2.6 - - - +
98A SER* 2.9 35.4 + - - +
179A VAL* 5.9 0.2 - - + -
180A PHE* 1.3 80.0 - - - +
182A GLY* 1.3 74.3 + - - +
333A GLU* 3.1 39.2 + - + +
335A ASN* 2.9 42.2 + - - +
337A ALA* 4.2 3.8 + - - +
151B SER* 2.9 51.3 + - - +
152B GLN* 5.2 1.6 + - - -
154B ASN* 4.0 21.3 - - - +
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Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL 3.7 7.4 - - - -
97A TYR* 3.7 8.3 - - - -
180A PHE* 3.8 18.3 - - - -
181A LYS* 1.3 97.2 + - - +
183A LEU* 1.3 63.1 + - - -
184A TRP* 3.9 3.6 + - - -
234A PHE* 3.9 14.2 - - - -
333A GLU 5.0 1.3 + - - +
334A ILE* 6.3 0.2 - - - +
337A ALA 4.5 1.6 - - - +
151B SER* 4.3 2.7 - - - -
152B GLN* 5.7 0.2 - - - -
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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