Contacts of the strand formed by residues 193 - 200 (chain B) in PDB entry 4OE4
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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A ARG* 6.1 0.4 - - - -
185B PRO* 3.6 36.5 - - + +
186B VAL* 3.3 29.4 - - - -
187B GLU* 3.3 28.7 - - + -
191B GLY 4.0 0.2 + - - -
192B THR* 1.3 72.2 - - - +
194B ASN* 1.3 61.1 + - - +
558B THR* 3.7 1.7 - - - +
559B LYS* 3.5 1.4 - - - -
560B GLU* 2.8 48.0 + - + +
562B PHE* 3.4 34.8 - + + -
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Residues in contact with ASN 194 (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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185B PRO* 3.0 8.5 - - - +
186B VAL* 2.9 43.8 + - + +
188B SER* 2.9 27.1 + - - -
192B THR* 3.2 23.4 + - - -
193B TRP* 1.3 76.4 - - - +
195B LYS* 1.3 62.2 + - - +
557B ASN* 6.2 0.8 - - + +
558B THR 3.3 4.6 - - - +
559B LYS* 2.7 39.4 + - - +
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Residues in contact with LYS 195 (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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505A ASP* 2.7 31.6 + - - -
517A ILE* 6.0 0.2 - - - -
184B GLN 5.5 0.7 - - - -
185B PRO* 4.2 19.5 - - + -
194B ASN* 1.3 76.4 - - - +
196B ALA* 1.3 62.8 + - - +
197B GLU* 3.6 23.9 + - + +
556B ARG 3.9 0.3 - - - +
557B ASN* 3.5 3.4 - - - +
558B THR* 2.8 56.4 + - + +
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Residues in contact with ALA 196 (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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183B GLN* 4.0 26.8 - - + +
184B GLN 5.9 0.6 + - - -
195B LYS* 1.3 79.3 - - - +
197B GLU* 1.3 62.2 + - - +
198B TYR* 5.8 1.6 - - + -
555B ILE* 3.6 17.3 - - + -
556B ARG 3.4 4.5 - - - -
557B ASN* 3.6 18.8 - - - +
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Residues in contact with GLU 197 (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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509A LYS* 6.1 2.5 - - + -
195B LYS* 3.6 26.9 + - + +
196B ALA* 1.3 74.8 - - - +
198B TYR* 1.3 63.5 + - - +
199B ARG* 3.7 3.8 + - + +
554B SER 3.6 0.3 - - - +
555B ILE* 3.6 6.0 - - - -
556B ARG* 2.7 87.0 + - + +
558B THR* 3.2 15.9 + - - -
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Residues in contact with TYR 198 (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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180B LEU* 3.3 56.9 - - + +
181B TYR* 3.9 34.4 + + + -
183B GLN* 5.7 4.3 - - + -
196B ALA* 5.8 1.3 - - + -
197B GLU* 1.3 74.7 - - - +
199B ARG* 1.3 62.9 + - - +
200B PRO* 4.1 1.0 - - - +
227B MET* 5.2 0.7 - - + +
550B SER* 6.2 2.2 - - - -
553B VAL* 3.6 33.7 - - + +
554B SER 3.5 1.8 - - - -
555B ILE* 3.6 39.9 - - + +
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Residues in contact with ARG 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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509A LYS* 2.4 52.4 + - + -
510A PHE* 3.5 33.0 + - + +
512A ALA 3.2 16.6 + - - -
513A GLY* 3.8 19.6 - - - +
197B GLU* 3.7 4.7 + - + +
198B TYR* 1.3 74.3 - - - +
200B PRO* 1.3 74.8 - - + +
553B VAL* 3.1 7.9 - - - +
554B SER* 2.8 61.0 + - - +
555B ILE 4.0 7.1 + - - -
556B ARG* 4.0 17.6 - - + +
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Residues in contact with PRO 200 (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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509A LYS* 5.8 0.7 - - + -
510A PHE* 3.3 23.7 - - + -
113B LYS* 3.9 9.0 - - - -
117B TYR* 4.1 22.9 - - + -
198B TYR 4.1 1.5 - - - +
199B ARG* 1.3 95.7 - - + +
201B LEU* 1.3 73.3 + - - +
202B GLU 3.6 0.2 + - - -
227B MET 3.5 18.0 - - - +
228B GLY 3.5 23.6 - - - +
229B ASN* 3.4 12.8 - - - +
552B PHE 3.6 9.9 - - - +
553B VAL* 4.4 0.2 - - - -
554B SER* 4.3 2.9 + - - -
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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