Contacts of the strand formed by residues 204 - 215 (chain T) in PDB entry 1V2J
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 LYS 204 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121T ILE* 3.4 4.0 - - - -
122T SER* 3.5 22.1 + - - +
123T LEU 3.9 16.9 + - - +
124T PRO* 4.1 21.8 - - + -
125T THR* 5.5 11.0 - - - +
200T VAL* 3.3 2.0 - - - +
201T CYS 3.0 31.8 + - - +
202T SER* 3.9 14.6 - - - +
203T GLY* 1.3 85.4 + - - +
209T LEU* 1.3 59.3 + - - +
210T GLN* 3.2 12.6 + - - +
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Residues in contact with LEU 209 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T SER* 3.7 9.9 - - - +
47T ILE* 4.3 7.2 - - + -
53T VAL* 3.4 33.4 - - + -
121T ILE* 3.0 21.7 - - + +
122T SER 2.9 15.0 + - - +
123T LEU* 4.5 8.5 - - + -
124T PRO* 3.0 24.4 - - + +
198T PRO* 3.7 26.9 - - + -
199T VAL 3.8 5.8 - - - +
200T VAL* 4.3 4.7 - - + -
204T LYS* 1.3 70.8 - - - +
210T GLN* 1.3 57.6 + - - +
211T GLY 3.4 24.9 - - - +
212T ILE* 5.4 1.8 - - + -
231T VAL* 3.6 16.5 - - + +
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Residues in contact with GLN 210 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124T PRO* 3.2 22.7 - - - +
127T SER 3.1 20.7 + - - +
128T CYS* 4.0 0.4 - - - +
129T ALA* 3.7 32.6 + - + +
162T ILE* 5.1 0.2 - - + -
181T PHE* 3.2 18.6 - - + -
199T VAL 2.9 5.5 + - - -
201T CYS* 3.8 32.3 - - + +
204T LYS* 3.2 17.3 + - - +
209T LEU* 1.3 72.6 - - - +
211T GLY* 1.3 59.0 + - - +
230T LYS* 4.0 1.1 - - - +
231T VAL* 3.1 25.0 + - - +
232T CYS* 3.9 15.2 - - - +
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Residues in contact with GLY 211 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181T PHE* 3.7 8.7 - - - -
198T PRO* 3.8 1.0 - - - +
199T VAL* 3.0 40.2 + - - +
209T LEU* 3.4 13.3 - - - +
210T GLN* 1.3 81.6 - - - +
212T ILE* 1.3 64.9 + - - +
229T THR 3.2 10.1 - - - -
231T VAL* 3.6 3.4 - - - +
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Residues in contact with ILE 212 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53T VAL* 3.9 19.1 - - + -
54T SER* 3.7 25.6 - - - +
55T ALA* 3.9 5.8 - - + +
102T ASP 4.3 1.6 - - - +
103T ILE* 3.8 26.5 - - + -
196T GLY* 3.6 31.6 - - - +
197T GLY 3.2 5.2 - - - +
199T VAL* 4.1 0.4 - - - +
209T LEU* 5.4 1.6 - - + -
211T GLY* 1.3 78.5 - - - +
213T VAL* 1.3 72.2 + - - +
214T SER* 3.0 4.9 + - - -
228T TYR* 3.3 7.0 - - - +
229T THR* 3.0 39.0 + - - +
231T VAL* 3.8 15.3 - - + -
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Residues in contact with VAL 213 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 3.8 15.5 - - + -
55T ALA* 4.0 2.8 - - - +
138T ILE* 4.0 18.6 - - + -
139T SER 5.1 1.6 - - - +
190T SER* 3.6 23.1 - - - +
194T ASP* 3.4 25.4 - - + +
195T SER* 3.4 21.1 - - - +
196T GLY 2.9 24.7 + - - +
197T GLY* 3.0 18.9 + - - +
198T PRO 4.6 1.6 - - - +
199T VAL* 4.5 0.4 - - + +
211T GLY 4.3 0.2 - - - -
212T ILE* 1.3 74.3 - - - +
214T SER* 1.3 60.1 + - - +
227T VAL 5.6 0.2 - - - +
228T TYR* 3.5 20.8 - - + -
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Residues in contact with SER 214 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 4.0 5.3 - - - -
57T HIS* 3.0 23.9 + - - -
99T LEU* 4.3 3.3 + - - +
102T ASP* 2.7 33.6 + - - +
180T MET* 5.7 1.1 - - - +
195T SER* 3.7 5.4 + - - -
212T ILE* 3.0 8.9 + - - -
213T VAL* 1.3 75.5 - - - +
215T TRP* 1.3 79.9 + - - +
227T VAL* 3.4 14.5 + - - -
228T TYR* 4.2 1.1 - - - -
229T THR* 3.9 14.8 - - - -
600T SO4 4.7 0.3 + - - -
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Residues in contact with TRP 215 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 3.7 23.9 + - + -
98T THR 4.8 4.3 - - - -
99T LEU* 3.6 29.9 - - + +
172T SER* 4.1 7.0 - - - -
174T ARG* 3.4 49.4 - - + -
175T ILE* 3.8 17.7 - - + -
180T MET* 3.6 21.9 - - + +
214T SER* 1.3 99.2 - - - +
216T GLY* 1.3 89.2 + - - +
217T SER* 4.8 4.3 - - - -
227T VAL* 2.8 62.6 + - + +
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Residues in contact with GLY 216 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 3.8 24.6 - - - -
215T TRP* 1.3 96.4 - - - +
217T SER* 1.3 61.2 + - - -
219T GLY 3.4 8.2 + - - -
225T PRO 4.6 10.8 - - - -
227T VAL* 4.7 0.9 - - - -
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Residues in contact with SER 217 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 4.7 0.6 + - - -
174T ARG* 6.2 2.2 - - - -
215T TRP* 4.6 6.1 - - - -
216T GLY* 1.3 68.9 - - - -
219T GLY* 1.3 61.9 + - - +
220T CYS 3.8 0.9 + - - -
221T GLN* 3.9 8.8 + - - +
224T LYS* 3.9 50.7 + - - +
225T PRO 5.1 1.6 + - - -
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Residues in contact with GLY 219 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 2.8 27.0 + - - -
192T GLN* 5.5 1.8 - - - -
216T GLY 3.4 3.6 + - - -
217T SER* 1.3 74.3 + - - +
220T CYS* 1.3 67.9 + - - -
221T GLN* 4.5 5.6 - - - -
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Residues in contact with CYS 220 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T BEN 3.7 7.9 - - - -
17T VAL* 4.3 8.5 - - + -
145T LYS 4.6 0.4 - - - +
146T SER* 3.6 16.7 + - - +
190T SER 4.1 2.2 - - - +
191T CYS* 2.0 59.7 - - + -
192T GLN* 3.9 11.9 - - - -
217T SER 3.8 1.0 + - - -
219T GLY* 1.3 83.8 - - - -
221T GLN* 1.3 94.3 + - - +
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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