Contacts of the strand formed by residues 198 - 205 (chain B) in PDB entry 3HI7
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A TRP* 3.6 36.2 + - + -
544A SER* 5.2 5.3 + - - -
189B PRO 4.7 0.2 - - - +
190B ARG* 2.8 32.2 + - - +
191B GLY* 3.2 4.6 + - - -
192B VAL* 4.1 8.9 - - - +
196B GLN* 3.0 41.9 + - + +
197B ARG* 1.3 79.0 - - - +
199B SER* 1.3 60.8 + - - +
200B TRP* 4.1 1.6 + - - -
220B LEU* 3.6 15.5 - - + +
221B VAL 3.2 6.3 - - - -
222B ASP* 4.0 16.6 + - - -
234B GLU* 2.8 45.0 + - - +
368B GLN* 5.5 0.7 + - - +
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Residues in contact with SER 199 (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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151B LEU* 5.8 1.1 - - - -
186B ASP* 4.7 0.2 - - - -
187B VAL 4.3 5.2 - - - -
190B ARG* 2.8 37.7 + - - +
198B ARG* 1.3 71.7 - - - +
200B TRP* 1.3 61.7 + - - +
201B LEU* 3.7 19.7 + - - +
219B LEU 3.4 2.6 - - - +
220B LEU* 3.6 3.1 - - - -
221B VAL* 2.9 33.0 + - - -
223B HIS* 2.8 30.4 + - - -
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Residues in contact with TRP 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A TRP* 3.3 53.4 - + + +
185B THR 4.0 0.5 - - - +
187B VAL* 3.0 47.6 + - + +
189B PRO 5.8 0.4 + - - -
198B ARG 4.1 1.3 + - - -
199B SER* 1.3 72.3 - - - +
201B LEU* 1.3 61.4 - - - +
202B ILE 4.3 0.2 + - - -
218B GLU* 3.6 28.3 - - + -
219B LEU 3.4 24.0 - - - -
220B LEU* 3.5 38.1 - - + +
235B GLN* 3.8 23.6 - - + -
237B TRP* 4.3 3.4 - - + -
242B PHE* 4.0 3.8 - + - -
364B PRO* 3.5 39.5 - - + +
365B ALA* 3.9 14.1 - - + -
368B GLN* 4.2 11.5 - - + +
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Residues in contact with LEU 201 (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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151B LEU* 5.0 11.2 - - + -
155B LEU* 3.9 26.5 - - + -
184B PHE* 3.8 29.6 - - + -
185B THR 3.5 2.5 - - - -
186B ASP* 3.5 29.4 - - + -
199B SER* 3.8 17.5 - - - +
200B TRP* 1.3 75.9 - - - +
202B ILE* 1.3 62.7 + - - +
203B ILE* 3.7 6.8 + - + +
218B GLU* 3.1 8.2 - - - -
219B LEU* 2.7 41.3 + - + +
221B VAL* 3.6 27.4 - - + -
365B ALA* 5.2 0.2 - - - -
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Residues in contact with ILE 202 (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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184B PHE* 3.2 4.2 - - - -
185B THR* 2.8 43.3 + - + +
187B VAL* 3.9 5.8 - - + -
201B LEU* 1.3 71.0 - - - +
203B ILE* 1.3 71.4 + - - +
204B GLN* 3.7 17.5 + - + +
214B PRO* 4.3 14.4 - - + -
217B LEU 4.9 0.4 - - - +
218B GLU* 4.0 17.0 - - + +
365B ALA* 3.5 31.0 - - + -
486B HIS* 3.7 30.7 - - + +
487B ALA 4.2 7.6 - - - +
488B THR* 4.1 15.9 - - + -
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Residues in contact with ILE 203 (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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155B LEU* 4.1 10.1 - - + -
166B PHE* 5.3 0.7 - - + -
174B PHE* 4.4 7.9 - - + -
182B LEU* 4.1 26.2 - - + -
183B ALA 3.5 7.6 - - - +
184B PHE* 3.9 21.8 - - + -
201B LEU* 4.3 6.7 - - + +
202B ILE* 1.3 75.5 - - - +
204B GLN* 1.3 62.5 - - - +
214B PRO* 3.4 6.2 - - - +
215B THR* 2.9 42.3 + - + +
216B GLY 4.6 0.2 + - - -
217B LEU* 3.1 45.7 + - + +
219B LEU* 4.0 22.2 - - + -
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Residues in contact with GLN 204 (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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182B LEU* 3.3 7.3 - - - +
183B ALA* 2.8 34.2 + - + +
184B PHE* 3.8 5.0 + - - -
185B THR* 2.6 41.9 + - - +
202B ILE* 3.9 18.6 - - + +
203B ILE* 1.3 79.3 - - - +
205B ARG* 1.3 62.2 + - - +
210B TYR* 3.7 26.5 - - + +
211B PHE* 3.6 24.9 + - - +
213B HIS 3.1 14.1 - - - +
214B PRO* 4.0 7.8 - - + +
215B THR* 3.9 6.7 - - - -
487B ALA 4.9 4.2 + - - -
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Residues in contact with ARG 205 (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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170B THR* 2.8 29.8 + - - -
172B PHE* 3.8 39.1 - - + -
181B CYS 4.2 0.2 - - - -
182B LEU* 4.4 3.8 - - + -
204B GLN* 1.3 70.9 - - - +
206B TYR* 1.3 59.9 + - - +
207B VAL* 3.0 14.3 + - + +
210B TYR* 3.4 17.5 - - - +
213B HIS* 2.9 37.9 + - + +
215B THR* 4.0 13.9 - - + +
263B LEU* 3.6 50.9 + - + +
504B HIS* 5.8 2.0 - - - -
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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