Contacts of the strand formed by residues 208 - 215 (chain B) in PDB entry 1H1B
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 LEU 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLN* 3.4 18.4 - - + +
123B LEU 4.4 5.4 - - - +
124B PRO* 3.8 31.4 - - + -
125B ALA 5.2 0.2 - - - +
128B ARG* 4.5 18.4 - - - +
200B VAL* 3.7 1.0 - - - -
201B CYS 3.0 28.4 + - - +
204B ASN 3.7 13.2 - - - +
205B GLY* 1.3 85.1 - - - +
209B ILE* 1.3 62.0 + - - +
210B HIS* 3.2 23.8 + - + +
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Residues in contact with ILE 209 (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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29B PHE* 4.3 13.5 - - + -
45B THR* 4.2 5.2 - - + +
53B MET* 3.9 21.1 - - + -
121B ALA* 3.9 24.0 - - + -
122B GLN 3.0 15.8 + - - +
123B LEU* 3.8 18.2 - - + -
124B PRO* 2.9 21.4 - - - +
198B PRO* 4.0 24.5 - - + -
199B LEU 3.7 2.0 - - - +
200B VAL* 4.6 8.5 - - + -
205B GLY 5.6 1.1 - - - +
208B LEU* 1.3 71.1 - - - +
210B HIS* 1.3 61.0 + - - +
211B GLY 3.5 21.8 - - - +
212B ILE* 5.1 0.4 - - + -
231B VAL* 3.4 12.2 - - + +
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Residues in contact with HIS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.6 24.9 - - + +
128B ARG* 3.6 38.3 + - + -
130B LEU* 3.6 32.9 - - + +
181B VAL* 4.1 10.9 - - - +
199B LEU* 3.0 8.0 + - + -
201B CYS* 3.8 41.0 + - + -
208B LEU* 3.2 29.2 + - + +
209B ILE* 1.3 75.4 - - - +
211B GLY* 1.3 57.7 + - - +
229B ALA 3.7 1.2 - - - +
230B PRO* 3.9 4.2 - - - +
231B VAL* 3.1 23.2 + - - -
232B ALA* 4.5 4.0 + - - +
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Residues in contact with GLY 211 (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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181B VAL* 5.4 0.4 - - - -
198B PRO* 3.1 6.4 - - - +
199B LEU* 2.7 43.3 + - - +
209B ILE* 3.4 7.4 - - - +
210B HIS* 1.3 82.3 - - - +
212B ILE* 1.3 62.5 + - - -
228B PHE* 3.9 9.9 - - - -
229B ALA 3.2 10.3 - - - -
231B VAL* 3.8 2.9 - - - -
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Residues in contact with ILE 212 (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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45B THR* 5.9 1.6 - - - +
53B MET* 3.6 23.3 - - + -
54B SER* 3.6 3.8 - - - +
55B ALA* 3.6 16.6 - - + +
102B ASP 5.1 0.2 - - - +
103B ILE* 3.4 45.1 - - + -
196B GLY* 3.3 41.1 - - - +
197B SER 3.2 4.3 - - - -
198B PRO* 5.3 1.3 - - + -
209B ILE* 5.1 0.2 - - + -
211B GLY* 1.3 77.7 - - - +
213B ALA* 1.3 63.9 + - - +
214B SER* 3.3 0.9 + - - -
228B PHE* 3.7 3.1 - - - +
229B ALA* 2.8 42.2 + - + +
231B VAL* 3.8 15.0 - - + -
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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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55B ALA* 3.8 6.4 - - - +
190B VAL* 5.0 9.2 - - + -
194B ASP* 3.5 25.1 - - + +
195B SER* 3.4 7.6 - - - -
196B GLY 2.9 22.9 + - - -
197B SER* 2.8 16.2 + - - +
212B ILE* 1.3 71.5 - - - +
214B SER* 1.3 58.2 + - - +
227B ALA 4.1 0.4 - - - -
228B PHE* 3.4 26.5 - - + -
400B 151 4.5 6.5 - - + -
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Residues in contact with SER 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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55B ALA* 5.1 0.2 - - - -
57B HIS* 5.6 0.5 - - - +
99B LEU* 3.6 13.9 - - - +
102B ASP* 2.6 40.5 + - - +
180B ASN* 5.0 2.7 + - - -
195B SER* 3.8 2.2 + - - -
212B ILE 3.9 7.2 - - - -
213B ALA* 1.3 74.8 - - - +
215B PHE* 1.3 76.3 + - - +
227B ALA 2.9 15.9 + - - -
229B ALA* 4.1 8.1 - - - -
400B 151 3.4 23.7 - - - +
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Residues in contact with PHE 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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99B LEU* 3.5 20.4 - + - +
177B ARG* 4.0 33.7 - - + -
180B ASN* 3.7 24.7 - - - -
190B VAL* 4.9 0.5 - - - +
214B SER* 1.3 94.7 - - - +
216B VAL* 1.3 70.0 + - - +
217B ARG* 3.6 28.7 - - + -
226B ASP* 3.9 0.9 - - - +
227B ALA* 2.9 49.1 + - + +
400B 151 3.5 48.6 - - + +
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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