Contacts of the strand formed by residues 198 - 201 (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 PRO 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.9 10.3 - - + -
30B MET* 3.5 21.1 - - - -
44B ALA 4.4 1.3 - - - +
45B THR* 2.9 27.7 - - - +
137B LEU 4.3 0.2 - - - +
138B ALA* 4.4 1.2 - - - +
139B MET* 3.7 40.6 + - + +
197B SER* 1.3 93.6 - - - +
199B LEU* 1.3 60.1 + - - +
200B VAL 4.0 1.1 + - - -
209B ILE* 4.0 23.1 - - + -
211B GLY 3.1 8.7 - - - +
212B ILE* 4.5 1.8 - - + -
228B PHE* 5.0 2.2 - - - -
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Residues in contact with LEU 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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136B CYS* 3.9 15.0 - - + -
137B LEU 3.6 11.9 - - - +
138B ALA* 4.0 10.3 - - + +
160B VAL* 4.1 3.6 - - + -
181B VAL* 4.2 19.1 - - + -
183B THR* 3.9 26.0 - - + -
198B PRO* 1.3 73.4 - - - +
200B VAL* 1.3 60.2 + - - +
201B CYS* 3.6 21.3 + - - -
209B ILE* 3.7 2.8 - - - -
210B HIS* 3.0 24.7 + - + -
211B GLY* 2.7 20.3 + - - +
228B PHE* 3.8 38.1 - - + -
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 5.2 2.7 - - + -
29B PHE* 3.7 23.6 - - + -
136B CYS* 3.3 1.6 - - - +
137B LEU* 2.8 40.8 + - + +
139B MET* 3.4 32.5 - - + -
198B PRO* 4.8 0.7 - - + +
199B LEU* 1.3 73.5 - - - +
201B CYS* 1.3 62.3 + - - +
205B GLY* 4.1 20.6 - - - +
208B LEU 3.7 5.6 - - - +
209B ILE* 4.6 6.3 - - + +
2E FUC 3.6 36.3 - - + +
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Residues in contact with CYS 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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130B LEU* 3.7 19.7 - - + -
134B VAL* 4.7 8.7 - - + -
136B CYS* 2.0 44.9 - - - -
199B LEU* 3.6 18.2 - - - -
200B VAL* 1.3 72.5 - - - +
204B ASN* 1.3 75.2 + - + +
205B GLY 2.9 1.8 + - - -
208B LEU* 3.0 19.0 + - - +
210B HIS* 3.8 24.0 + - + -
2E FUC 3.4 3.8 - - - +
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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