Contacts of the strand formed by residues 172 - 182 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL* 5.4 0.7 - - + -
105B LEU* 3.7 47.1 - - + -
106B TYR 3.1 18.2 - - - +
107B ALA* 3.8 17.9 - - + -
129B LEU* 4.5 4.3 - - - -
134B PHE* 4.5 0.7 - - - -
170B THR 3.9 0.2 - - - -
171B ALA* 1.3 82.5 - - - +
173B VAL* 1.3 63.9 + - - +
312B LEU* 3.7 30.5 - - + -
315B ILE* 4.0 11.2 - - + -
321B LEU* 4.0 14.8 - - + -
322B LYS 3.3 15.9 + - - +
323B ILE* 3.6 13.9 - - + -
324B SER* 2.7 33.8 + - - -
325B GLN 3.5 0.5 + - - -
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Residues in contact with VAL 173 (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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104B ARG 3.7 1.2 - - - +
105B LEU* 3.5 4.6 - - - -
106B TYR* 2.8 38.6 + - - +
134B PHE* 3.7 14.6 - - + -
145B ILE* 4.5 6.3 - - + -
161B LEU* 4.1 22.2 - - + -
166B VAL* 3.9 14.6 - - + -
170B THR* 3.7 24.0 - - + -
172B MET* 1.3 78.1 - - - +
174B LEU* 1.3 63.9 + - - +
175B VAL* 4.0 22.8 + - + -
325B GLN* 3.4 19.3 - - + +
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Residues in contact with LEU 174 (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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37B ALA* 4.0 33.0 - - + +
38B LEU* 4.9 11.0 - - + -
40B MET* 4.8 3.8 - - + -
41B VAL* 4.9 11.0 - - + -
104B ARG 3.6 18.2 - - - +
105B LEU* 3.8 22.0 - - + -
172B MET 4.3 0.4 - - - -
173B VAL* 1.3 74.4 - - - +
175B VAL* 1.3 69.5 + - - +
176B ASN* 4.9 2.7 - - + -
293B LEU* 4.6 12.3 - - + -
297B LEU* 6.1 1.1 - - + -
323B ILE* 4.6 10.5 - - + +
325B GLN 2.9 12.3 + - - +
326B ALA* 3.3 18.5 - - + -
327B VAL* 3.0 29.1 + - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA 4.0 1.6 - - - +
103B SER* 3.2 2.6 + - - -
104B ARG 2.9 42.9 + - - +
106B TYR* 4.2 12.8 - - + -
145B ILE* 3.8 23.6 - - + -
148B TRP* 4.0 27.4 - - + -
149B VAL* 4.0 15.0 - - + -
160B VAL* 4.3 8.1 - - + -
161B LEU* 4.9 0.7 - - + -
173B VAL* 4.0 11.9 - - + -
174B LEU* 1.3 78.6 - - - +
176B ASN* 1.3 62.5 + - - +
177B ALA* 6.1 0.2 - - + -
327B VAL* 3.8 19.3 - - + -
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Residues in contact with ASN 176 (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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33B ALA* 3.1 30.8 + - - +
34B ILE* 3.6 12.8 + - - +
37B ALA* 3.8 12.7 - - + +
101B LEU* 4.2 1.4 - - - +
102B ALA 3.6 2.0 - - - -
103B SER* 3.1 27.4 + - - +
160B VAL* 6.0 0.4 - - - +
174B LEU* 4.9 2.5 - - + -
175B VAL* 1.3 75.8 - - - +
177B ALA* 1.3 61.0 + - - +
293B LEU* 4.7 7.6 - - + -
327B VAL* 2.9 15.8 + - - +
328B HIS* 2.6 37.9 + - - +
329B ALA 3.0 21.9 + - - -
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Residues in contact with ALA 177 (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 SER 3.8 0.2 - - - +
101B LEU* 3.5 3.8 - - - +
102B ALA* 2.7 47.7 + - + +
149B VAL* 3.7 31.0 - - + -
153B THR* 4.7 2.6 - - + +
157B ILE* 3.9 11.9 - - + -
160B VAL* 5.5 2.7 - - + -
175B VAL* 6.1 0.2 - - + -
176B ASN* 1.3 76.3 - - - +
178B ILE* 1.3 62.4 + - - +
329B ALA* 3.2 15.3 - - + +
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Residues in contact with ILE 178 (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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30B CYS* 3.7 26.5 - - + -
33B ALA* 4.6 2.5 - - + -
99B PHE* 3.2 55.0 - - + -
100B SER 2.7 31.0 - - - +
101B LEU* 4.0 8.3 - - + +
153B THR* 5.5 0.2 - - - -
157B ILE* 3.7 4.1 - - - +
177B ALA* 1.3 78.4 - - - +
179B VAL* 1.3 69.5 + - - +
328B HIS* 4.4 7.0 - - + -
329B ALA 2.9 12.5 + - - +
330B ALA* 3.4 10.9 - - + -
331B HIS 3.0 24.4 + - - +
378B PHE* 3.8 13.2 - - + -
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Residues in contact with VAL 179 (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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154A ASN* 4.7 13.9 - - - +
98B SER 3.7 0.9 - - - +
99B PHE* 3.4 3.3 - - - -
100B SER* 2.8 44.0 + - - +
153B THR* 3.7 36.1 - - + +
156B ILE* 4.1 19.3 - - + -
157B ILE* 4.0 9.2 - - + -
178B ILE* 1.3 81.5 - - - +
180B PHE* 1.3 68.5 + - - +
181B LYS* 5.8 1.8 - - + -
331B HIS* 3.3 22.2 - - + +
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Residues in contact with PHE 180 (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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97B TYR* 4.0 14.6 - + + -
98B SER 3.3 14.1 - - - -
99B PHE* 4.2 11.2 - + + -
179B VAL* 1.3 80.4 - - - +
181B LYS* 1.3 63.7 + - - +
182B GLY* 3.8 21.5 - - - -
234B PHE* 3.9 15.0 - + - -
239B MET* 3.5 42.2 - - + -
331B HIS* 3.0 7.4 + - - -
332B ALA* 3.4 32.0 - - + +
333B GLU 3.7 4.4 + - - -
334B ILE* 5.4 5.8 - - + -
368B ILE* 3.8 30.1 - - + -
378B PHE* 3.5 32.1 - + + -
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Residues in contact with LYS 181 (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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151A SER* 3.2 47.4 + - - +
152A GLN* 5.2 0.5 - - - +
154A ASN* 5.5 8.5 - - - +
155A GLY 6.0 0.9 - - - +
97B TYR* 3.3 3.1 - - - +
98B SER* 2.8 39.6 + - - +
179B VAL* 5.8 2.2 - - + -
180B PHE* 1.3 80.2 - - - +
182B GLY* 1.3 74.8 + - - +
333B GLU* 3.4 41.3 + - + +
335B ASN* 3.1 38.6 - - - +
337B ALA* 4.5 2.2 - - - +
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Residues in contact with GLY 182 (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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151A SER* 4.4 2.0 - - - -
96B VAL 3.8 0.2 - - - -
97B TYR* 3.8 13.9 - - - -
180B PHE* 3.8 17.1 - - - -
181B LYS* 1.3 94.3 + - - +
183B LEU* 1.3 63.6 + - - -
184B TRP* 3.8 4.0 + - - -
234B PHE* 3.8 17.3 - - - -
333B GLU 5.1 1.9 + - - +
334B ILE* 6.3 0.2 - - - +
335B ASN* 5.3 0.3 + - - -
337B ALA 4.4 2.4 - - - +
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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