Contacts of the strand formed by residues 212 - 222 (chain B) in PDB entry 1U1C
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 ARG 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.0 12.8 + - - +
88B THR* 2.9 31.5 + - - +
89B PHE* 2.7 34.1 + - - +
133B ASP* 3.6 22.2 - - - +
135B GLU* 2.8 51.3 + - - +
136B CYS* 3.8 14.1 - - - -
210B GLY 4.2 2.7 + - - +
211B LEU* 1.3 73.2 - - - +
213B ALA* 1.3 55.4 + - - +
252B LEU* 3.8 35.7 + - - +
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Residues in contact with ALA 213 (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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89B PHE* 3.1 8.7 - - + +
131B VAL 6.0 0.2 - - - +
132B ALA* 3.7 4.7 - - - +
133B ASP* 2.9 33.8 + - - +
136B CYS* 3.6 6.0 - - - +
202B LEU* 4.3 9.2 - - + +
203B LEU* 3.9 20.2 - - + +
206B CYS* 3.6 29.8 - - + -
211B LEU 3.8 1.4 + - - -
212B ARG* 1.3 76.9 - - - +
214B GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 214 (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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89B PHE 2.8 9.5 + - - +
90B LEU* 3.9 3.4 - - - -
91B ARG* 2.9 28.3 + - - +
132B ALA* 4.7 4.5 - - - -
136B CYS* 3.7 18.5 - - - +
137B THR* 5.0 0.4 - - - -
140B LEU* 3.8 13.9 - - - -
202B LEU* 4.1 3.5 - - - +
203B LEU* 4.6 2.2 - - - -
213B ALA* 1.3 73.5 - - - +
215B MET* 1.3 62.1 + - - +
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Residues in contact with MET 215 (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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91B ARG* 3.2 51.1 - - + +
109B VAL* 3.6 9.4 - - - +
110B THR* 3.0 60.1 + - - +
132B ALA* 4.9 0.4 - - - +
137B THR* 5.7 0.2 + - - -
140B LEU* 3.5 6.6 - - - +
156B THR* 5.5 0.2 - - + -
194B ASN* 5.6 0.4 - - - +
196B GLU* 3.5 22.9 - - + +
199B SER* 3.8 14.6 - - - -
202B LEU* 5.2 0.9 - - + -
203B LEU* 4.4 16.7 - - + +
214B GLY* 1.3 74.4 - - - +
216B VAL* 1.3 77.9 + - - +
217B ALA* 3.9 15.3 - - + -
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Residues in contact with VAL 216 (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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91B ARG 3.1 18.2 + - - +
92B ILE* 3.8 19.7 - - + -
93B GLY 2.9 22.2 + - - -
107B VAL* 3.5 24.0 - - + -
108B LEU 3.3 15.0 - - - +
109B VAL* 3.9 16.2 - - + -
140B LEU* 3.7 25.8 - - + -
215B MET* 1.3 78.0 - - - +
217B ALA* 1.3 62.0 + - - +
241B ALA 4.3 4.0 - - - +
244B ILE* 4.2 6.5 - - + -
245B VAL* 4.1 11.4 - - + +
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Residues in contact with ALA 217 (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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92B ILE* 4.8 1.3 - - - -
93B GLY 3.3 18.6 - - - +
94B THR 4.3 0.2 - - - -
95B THR* 3.9 25.6 - - + -
107B VAL* 3.5 4.9 - - - +
108B LEU* 2.9 37.6 + - + +
194B ASN* 4.9 3.6 - - - +
215B MET* 3.9 15.3 - - + -
216B VAL* 1.3 77.9 - - - +
218B GLY* 1.3 60.7 + - - +
219B VAL 4.0 0.3 + - - -
241B ALA* 4.3 6.5 - - - -
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Residues in contact with GLY 218 (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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93B GLY 3.1 9.8 + - - -
94B THR* 3.7 5.1 - - - +
95B THR* 3.2 22.3 + - - -
106B ASP 3.7 5.8 - - - -
107B VAL* 4.8 0.4 - - - -
217B ALA* 1.3 72.5 - - - +
219B VAL* 1.3 63.7 + - - -
220B ILE* 3.4 4.2 + - - +
237B THR* 3.7 15.7 + - - -
238B GLU* 5.8 0.7 - - - -
241B ALA* 3.8 19.2 - - - +
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Residues in contact with VAL 219 (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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95B THR* 3.8 8.5 - - + +
97B ALA* 4.0 12.6 - - + -
102B ILE* 3.9 14.1 - - + -
103B ASN 3.5 20.6 - - - +
104B VAL* 3.4 9.2 - - - +
105B GLY 2.8 26.7 + - - -
106B ASP 2.9 23.2 + - - +
108B LEU* 3.7 34.3 - - + -
218B GLY* 1.3 68.9 - - - -
220B ILE* 1.3 58.3 + - - +
221B VAL 3.4 25.1 - - - +
222B ASN* 4.7 1.1 - - + +
237B THR* 3.3 7.2 + - - -
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Residues in contact with ILE 220 (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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94B THR* 3.9 25.1 - - + +
95B THR 3.3 16.8 + - - +
104B VAL* 3.5 20.0 - - - +
218B GLY 3.4 4.7 + - - +
219B VAL* 1.3 73.0 - - - +
221B VAL* 1.3 65.4 + - + +
226B GLN* 5.5 0.3 - - - -
229B PRO* 4.0 13.6 - - + +
230B ASN 4.6 2.4 + - - -
234B MET* 3.8 48.1 - - + +
237B THR* 3.5 24.2 - - + +
238B GLU* 5.4 2.7 - - + +
5011B BAU 3.7 34.3 - - + -
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Residues in contact with VAL 221 (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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95B THR 3.7 0.8 + - - -
96B GLY* 3.3 15.6 - - - -
97B ALA 2.9 22.9 + - - -
104B VAL* 4.1 1.6 - - - -
219B VAL* 3.4 10.7 - - - +
220B ILE* 1.3 84.4 - - - +
222B ASN* 1.3 65.4 + - - +
223B ARG* 4.6 5.2 - - - +
226B GLN* 3.6 31.6 - - + +
227B GLU* 3.4 33.2 - - - +
228B ILE 4.1 0.2 - - - -
229B PRO* 4.1 9.9 - - + -
5011B BAU 3.8 27.6 - - + +
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Residues in contact with ASN 222 (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 ALA* 3.6 17.4 - - + +
99B GLN 2.8 19.6 + - - -
100B PRO* 4.6 0.2 - - - +
102B ILE 2.5 29.0 + - - +
104B VAL* 4.1 4.2 - - + +
219B VAL* 5.1 1.6 - - + -
221B VAL* 1.3 74.1 - - - +
223B ARG* 1.3 55.0 + - - +
224B THR* 2.5 42.8 + - - +
225B GLN* 3.1 29.4 + - + +
226B GLN* 2.8 46.1 + - - +
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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