Contacts of the strand formed by residues 172 - 182 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D VAL* 5.7 0.7 - - + -
105D LEU* 3.8 33.2 - - + -
106D TYR 3.2 12.8 - - - +
107D ALA* 3.8 20.2 - - + -
129D LEU* 4.5 4.9 - - - -
134D PHE* 4.4 0.7 - - - -
171D ALA* 1.3 82.8 - - - +
173D VAL* 1.3 65.2 + - - +
312D LEU* 3.6 15.5 - - + -
315D ILE* 4.2 16.8 - - + -
321D LEU* 3.1 37.5 - - + -
322D LYS 3.2 17.5 + - - +
323D ILE* 3.6 14.1 - - + -
324D SER* 2.7 34.2 + - - -
325D GLN 3.6 0.2 + - - -
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Residues in contact with VAL 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ARG 3.6 1.7 - - - +
105D LEU* 3.4 6.5 - - - -
106D TYR* 2.9 37.5 + - + +
134D PHE* 3.7 16.6 - - + -
145D ILE* 4.6 2.9 - - + -
161D LEU* 4.0 32.8 - - + -
166D VAL* 4.1 10.3 - - + -
170D THR* 3.5 24.5 - - + -
172D MET* 1.3 79.6 - - - +
174D LEU* 1.3 63.8 + - - +
175D VAL* 4.0 13.2 + - + -
325D GLN* 3.4 21.1 - - + +
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Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ALA* 3.9 35.4 - - + +
38D LEU* 4.3 20.2 - - + -
40D MET* 6.1 1.6 - - + -
41D VAL* 4.8 3.8 - - + -
103D SER* 4.9 0.4 - - - +
104D ARG 3.6 13.2 - - - +
105D LEU* 3.8 23.1 - - + -
173D VAL* 1.3 73.5 - - - +
175D VAL* 1.3 71.1 + - - +
176D ASN* 5.0 2.5 - - + -
293D LEU* 4.5 9.2 - - + -
297D LEU* 6.1 0.2 - - + -
306D PHE* 6.5 0.2 - - + -
323D ILE* 4.5 14.8 - - + +
325D GLN 2.8 14.8 + - - +
326D ALA* 3.3 18.7 - - + -
327D VAL* 3.0 26.3 + - - +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ALA 4.0 1.8 - - - +
103D SER* 3.2 3.8 + - - -
104D ARG 2.9 49.5 + - - +
106D TYR* 4.1 12.8 - - + -
145D ILE* 3.7 24.0 - - + -
148D TRP* 4.0 20.0 - - + -
149D VAL* 4.1 15.0 - - + -
160D VAL* 4.2 10.1 - - + -
161D LEU* 4.5 2.0 - - + -
173D VAL* 4.0 11.6 + - + -
174D LEU* 1.3 77.9 - - - +
176D ASN* 1.3 61.3 + - - +
327D VAL* 3.8 18.6 - - + -
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Residues in contact with ASN 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA* 3.1 38.6 + - - +
34D ILE* 3.5 5.0 + - - +
37D ALA* 3.7 13.7 - - + +
101D LEU* 4.1 2.0 - - - +
102D ALA 3.5 1.6 - - - -
103D SER* 3.1 26.5 + - - -
160D VAL* 5.9 1.1 - - - +
174D LEU* 5.0 1.6 - - + -
175D VAL* 1.3 76.0 - - - +
177D ALA* 1.3 58.0 + - - +
293D LEU* 4.8 7.6 - - + -
327D VAL* 3.0 15.5 + - - +
328D HIS* 2.7 37.1 + - - +
329D ALA 3.0 22.5 + - - -
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D SER 3.7 0.2 - - - +
101D LEU* 3.5 0.5 - - - +
102D ALA* 2.8 41.4 + - + +
149D VAL* 3.8 25.8 - - + -
153D THR* 4.3 6.4 - - + +
157D ILE* 3.4 24.9 - - + -
160D VAL* 5.2 2.9 - - + -
176D ASN* 1.3 76.2 - - - +
178D ILE* 1.3 68.6 + - - +
329D ALA* 3.2 8.3 - - + +
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Residues in contact with ILE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D CYS* 3.5 16.8 - - + -
33D ALA* 3.6 14.6 - - + -
99D PHE* 4.2 13.2 - - + -
100D SER 3.1 8.3 - - - +
101D LEU* 3.1 37.9 - - + -
157D ILE* 3.5 6.1 - - - +
177D ALA* 1.3 73.5 - - - +
179D VAL* 1.3 64.5 + - - +
328D HIS* 4.4 3.6 - - + -
329D ALA 3.0 8.4 + - - +
330D ALA* 3.1 28.9 - - + -
331D HIS 3.0 17.5 + - - +
378D PHE* 3.1 28.3 - - + -
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Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASN* 4.4 17.9 - - - +
98D SER 3.7 0.9 - - - +
99D PHE* 3.4 5.4 - - - -
100D SER* 2.8 41.8 + - - +
153D THR* 3.6 38.1 - - + +
156D ILE* 3.6 31.6 - - + -
157D ILE* 4.1 7.6 - - + -
178D ILE* 1.3 80.5 - - - +
180D PHE* 1.3 67.2 + - - +
331D HIS* 3.2 15.3 - - + +
378D PHE* 5.2 0.4 - - - -
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Residues in contact with PHE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TYR* 4.0 20.0 - + + -
98D SER 3.3 13.0 - - - -
99D PHE* 4.2 11.2 - + + -
179D VAL* 1.3 80.3 - - - +
181D LYS* 1.3 62.8 + - - +
182D GLY* 3.7 24.2 - - - -
234D PHE* 4.0 20.9 - + - -
239D MET* 3.9 29.2 - - + -
331D HIS* 2.9 8.0 + - - +
332D ALA* 3.3 34.2 - - + +
333D GLU 3.6 4.7 + - - -
334D ILE* 5.3 5.2 - - + -
368D ILE* 3.8 29.6 - - + -
378D PHE* 3.5 31.0 - + + -
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Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLU* 5.9 0.4 - - - -
151C SER* 3.3 48.6 + - - +
154C ASN* 4.2 20.0 - - - +
155C GLY 5.9 0.7 - - - +
97D TYR* 3.3 2.1 - - - +
98D SER* 2.7 38.0 + - - +
180D PHE* 1.3 78.0 - - - +
182D GLY* 1.3 75.9 + - - +
333D GLU* 3.5 38.5 + - + +
335D ASN* 3.0 41.4 - - - +
337D ALA* 4.3 4.0 - - - +
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Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C SER* 4.4 3.4 - - - -
96D VAL 3.8 0.7 - - - -
97D TYR* 3.6 17.0 - - - -
180D PHE* 3.7 18.0 - - - -
181D LYS* 1.3 93.4 + - - +
183D LEU* 1.3 62.6 + - - -
184D TRP* 4.0 3.5 + - - -
234D PHE* 3.9 12.7 - - - -
333D GLU 5.1 1.9 + - - +
334D ILE* 6.1 0.4 - - - +
337D ALA 4.5 1.6 - - - +
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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