Contacts of the strand formed by residues 198 - 207 (chain K) in PDB entry 3IT8
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 198 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190K GLY 4.4 5.4 - - - +
191K ASN 4.1 3.4 - - - +
192K GLU* 3.4 16.4 - - + +
193K LEU 5.5 0.4 - - - -
196K GLY 5.3 0.6 - - - -
197K ASN* 1.3 85.3 + - + +
199K THR* 1.3 71.4 + - - +
200K LEU* 4.9 1.3 - - + -
270K ARG* 3.9 6.4 - - - -
271K THR* 2.9 52.0 + - + +
278K GLN* 3.7 21.3 - - - +
296K SER* 3.8 13.7 - - - -
297K GLU* 3.0 41.5 - - - +
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Residues in contact with THR 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K GLY* 3.3 5.2 - - - -
191K ASN* 3.1 53.6 + - + +
192K GLU* 3.7 3.1 - - - +
193K LEU* 4.0 30.4 - - + +
198K MET* 1.3 79.7 + - - +
200K LEU* 1.3 62.4 + - - +
268K LEU* 3.8 27.3 - - + +
269K VAL 3.2 15.2 + - - -
270K ARG* 4.6 4.1 - - - +
271K THR* 3.9 0.4 - - - -
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Residues in contact with LEU 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K VAL* 3.9 15.3 - - + -
189K THR 3.6 13.0 - - - +
190K GLY* 3.9 3.1 - - - -
198K MET* 4.9 2.0 - - + -
199K THR* 1.3 73.6 - - - +
201K GLU* 1.3 59.5 + - - +
202K CYS 4.2 0.7 - - - -
216K TRP* 3.8 17.7 - - + -
267K ASP 3.8 0.5 - - - +
268K LEU* 3.3 4.9 - - - +
269K VAL* 2.7 44.1 + - + +
271K THR* 3.5 15.9 + - - +
278K GLN* 4.0 4.9 - - + +
279K PRO* 3.4 46.0 - - + +
295K CYS 4.1 0.4 - - - +
296K SER* 2.9 35.9 - - - +
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Residues in contact with GLU 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K LYS 3.5 2.1 - - - +
188K VAL* 3.2 5.2 - - - -
189K THR* 2.7 44.8 + - - +
191K ASN* 3.5 22.8 + - - +
200K LEU* 1.3 74.4 - - - +
202K CYS* 1.3 60.2 + - - +
203K THR* 3.4 22.6 + - + +
266K THR* 3.9 27.0 + - + +
267K ASP 3.4 3.6 - - - +
268K LEU* 3.4 21.3 - - + +
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Residues in contact with CYS 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K VAL* 4.0 21.1 - - - -
187K LYS 3.8 2.5 - - - -
188K VAL* 4.1 4.5 - - - +
201K GLU* 1.3 71.2 - - - +
203K THR* 1.3 61.6 + - - +
204K VAL* 4.2 5.2 + - - +
214K THR* 4.2 1.8 - - - -
216K TRP* 3.4 17.7 - - + -
265K LEU* 4.1 1.0 - - - +
266K THR* 3.6 1.0 - - - -
267K ASP* 2.7 45.0 + - + +
281K CYS* 2.0 50.0 - - - -
283K VAL* 4.1 6.3 - - - -
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Residues in contact with THR 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K THR 3.4 1.7 - - - +
186K VAL* 3.3 5.7 - - - +
187K LYS* 3.0 39.1 + - + +
189K THR* 5.2 4.7 - - - +
201K GLU* 3.4 32.5 - - + +
202K CYS* 1.3 79.0 - - - +
204K VAL* 1.3 63.3 + - - +
205K ASN* 3.6 21.2 + - - -
265K LEU 3.3 9.2 - - - -
266K THR* 4.2 7.2 - - - +
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Residues in contact with VAL 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184K PRO* 3.2 35.2 - - + -
185K THR 3.4 2.5 - - - -
186K VAL* 4.1 10.1 - - + -
202K CYS* 4.7 5.2 - - - +
203K THR* 1.3 77.8 - - - +
205K ASN* 1.3 60.4 + - - +
207K PHE* 3.5 18.6 - - + -
212K VAL* 4.9 3.6 - - + -
214K THR* 5.5 0.9 - - - +
264K SER* 3.4 5.0 - - - -
265K LEU* 2.8 58.1 + - + +
283K VAL* 4.0 33.0 - - + -
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Residues in contact with ASN 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K THR 4.5 0.2 - - - +
184K PRO* 3.0 19.3 - - - +
185K THR* 2.7 32.3 + - - +
187K LYS* 4.2 23.0 - - - +
203K THR* 3.6 21.3 + - - -
204K VAL* 1.3 77.3 - - - +
206K SER* 1.3 78.5 + - - +
207K PHE 3.8 0.7 - - - -
264K SER* 3.8 10.3 + - - +
265K LEU 5.2 0.5 - - - +
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Residues in contact with SER 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K THR* 3.3 17.0 - - - +
183K THR 3.6 6.9 - - - +
205K ASN* 1.3 79.4 + - - +
207K PHE* 1.3 57.4 + - - +
257K ASP* 3.2 14.8 - - - -
258K LYS* 4.6 8.8 + - - -
262K THR* 2.6 27.7 + - - -
263K TYR 2.8 9.3 + - - -
264K SER* 3.0 11.1 + - - -
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Residues in contact with PHE 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K THR 3.1 12.3 - - - +
184K PRO* 3.5 17.0 - - + -
204K VAL* 3.5 39.9 - - + -
206K SER* 1.3 73.4 - - - +
208K TYR* 1.3 61.9 + - - +
209K PRO 3.5 14.4 - - - -
210K PRO* 3.6 17.9 - - + -
212K VAL* 3.4 27.4 - - + -
254K ILE* 4.3 6.3 - - + -
262K THR* 3.4 4.3 - - - -
263K TYR* 2.8 52.8 + - + -
264K SER 4.1 1.3 - - - -
265K LEU* 3.7 24.2 - - + -
285K HIS* 3.7 9.9 - - + -
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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