Contacts of the strand formed by residues 207 - 215 (chain C) in PDB entry 2JET
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 TRP 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLY* 3.1 31.3 + - - +
4A PRO* 4.1 7.6 - - + +
8A PRO* 3.7 33.4 - - + +
10A LEU* 4.4 12.6 - - + -
27B TRP* 4.0 8.7 - + - -
29B TRP* 3.5 34.3 - + + -
121B VAL* 3.2 16.1 - - + +
122B CYS* 3.5 8.0 + - - -
135B VAL 5.5 2.0 - - - -
136B CYS* 5.0 2.5 - - - -
137B ALA* 3.8 23.1 - - + -
200C VAL* 3.4 38.4 - - + -
201C CYS* 3.7 3.4 - - - -
202C GLN* 3.3 47.7 + - + +
206C VAL* 1.3 69.0 - - - +
208C THR* 1.3 59.7 + - - +
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Residues in contact with THR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 4.4 1.6 - - - -
122B CYS* 3.4 10.6 - - + +
123B LEU 3.7 2.7 - - - +
124B PRO* 3.4 43.1 - - + -
130B PHE* 3.9 12.3 - - + -
200C VAL* 3.3 3.4 - - - -
201C CYS* 2.8 37.8 + - - +
203C LYS* 3.5 15.1 - - + +
206C VAL* 3.4 18.5 + - - +
207C TRP* 1.3 74.5 + - - +
209C LEU* 1.3 62.7 + - - +
210C ALA* 3.1 6.1 + - - +
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 4.0 9.2 - - - +
47B ILE* 4.7 1.1 - - + -
53B VAL* 3.3 35.2 - - + -
121B VAL* 4.2 8.2 - - + +
122B CYS 3.0 16.6 + - - +
123B LEU* 3.7 19.5 - - + -
124B PRO* 3.3 20.0 - - - +
198C PRO* 3.8 27.1 - - + -
199C LEU 3.9 4.9 - - - +
200C VAL* 4.3 6.7 - - + -
208C THR* 1.3 69.0 - - - +
210C ALA* 1.3 60.1 + - - +
211C GLY 3.4 23.3 - - - +
212C ILE* 4.3 12.8 - - + -
231C VAL* 3.5 13.6 - - + +
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 3.5 35.7 - - + -
162C ILE* 5.4 1.8 - - + -
181C THR* 4.4 7.9 + - + -
199C LEU* 2.9 13.0 + - + +
201C CYS* 3.4 32.3 - - - -
208C THR 3.1 3.6 + - - +
209C LEU* 1.3 73.9 - - - +
211C GLY* 1.3 58.3 + - - +
229C SER 3.9 0.2 - - - +
230C ARG* 4.2 4.0 - - - +
231C VAL* 3.2 23.5 + - - +
232C THR* 4.6 1.9 + - - +
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Residues in contact with GLY 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C THR* 5.4 1.6 - - - -
199C LEU* 2.9 42.6 + - - +
209C LEU* 3.4 11.7 - - - +
210C ALA* 1.3 78.7 - - - +
212C ILE* 1.3 65.2 + - - -
228C TYR* 4.1 9.2 - - - -
229C SER 3.4 9.4 - - - -
230C ARG* 5.2 0.4 - - - -
231C VAL* 3.8 1.6 - - - -
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Residues in contact with ILE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 3.4 33.7 - - + -
54B THR* 3.8 13.5 - - - +
55B ALA* 3.9 4.7 - - + +
102B ASP 4.9 0.2 - - - +
103B ILE* 3.7 26.2 - - + -
196C GLY* 3.6 32.1 - - - +
197C GLY 3.5 4.5 - - - +
209C LEU* 4.3 8.5 - - + -
211C GLY* 1.3 79.0 - - - +
213C VAL* 1.3 68.6 + - - +
214C SER 3.1 0.5 + - - -
228C TYR* 3.3 3.4 - - - +
229C SER* 2.7 44.1 + - - +
231C VAL* 3.8 15.0 - - + -
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ALA* 3.7 5.0 - - - +
57B HIS* 3.5 7.8 - - - -
138B THR* 4.6 3.4 - - - +
144B THR* 5.4 3.8 - - + -
190C SER 5.5 1.8 - - - +
193C GLY* 4.4 18.2 - - - +
194C ASP 3.1 28.3 - - - +
195C SER* 3.9 10.3 - - - +
196C GLY 3.0 18.0 + - - +
197C GLY* 3.1 18.6 + - - +
198C PRO 4.9 0.2 - - - +
212C ILE* 1.3 70.0 - - - +
214C SER* 1.3 65.5 + - - +
215C TRP* 4.7 1.8 - - - +
217C SER* 4.8 16.6 - - - +
227C VAL 5.1 0.7 - - - +
228C TYR* 3.5 30.6 - - + -
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Residues in contact with SER 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B HIS* 3.2 25.5 + - - -
99B VAL* 3.6 5.5 + - - +
102B ASP* 2.6 33.0 + - - +
146B TYR* 4.6 3.1 - - - +
180C MET* 6.4 0.9 - - - -
195C SER* 4.8 0.9 + - - -
212C ILE 3.1 2.7 + - - -
213C VAL* 1.3 75.6 - - - +
215C TRP* 1.3 83.1 + - - +
227C VAL* 3.2 15.1 + - - -
228C TYR 4.3 1.1 - - - -
229C SER* 3.7 18.4 - - - -
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Residues in contact with TRP 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR 5.5 2.0 - - - -
99B VAL* 3.6 31.8 + - + +
146B TYR* 4.6 17.3 - - + -
172C TRP* 3.6 35.0 - + - -
175C LYS* 4.1 26.0 - - + -
176C ILE* 3.8 17.0 - - + -
180C MET* 4.2 10.6 - - + +
213C VAL* 4.7 3.5 - - - +
214C SER* 1.3 97.7 + - - +
216C GLY* 1.3 67.3 + - - +
217C SER* 3.3 9.0 + - - +
227C VAL* 2.7 74.6 + - + +
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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