Contacts of the strand formed by residues 192 - 198 (chain A) in PDB entry 3EYF
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 VAL 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LYS 3.5 0.7 - - - +
151A VAL* 3.3 8.1 - - - +
152A ASP* 2.5 56.9 + - - +
153A ASN* 5.5 8.3 - - - +
191A LYS* 1.3 84.5 - - + +
193A TYR* 1.3 70.3 + - - +
194A ALA* 4.9 5.4 - - + -
209A SER* 4.8 9.9 - - - +
210A PHE 3.6 7.4 - - - +
211A ASN* 4.0 17.0 - - - +
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 3.7 6.6 - - + +
133A VAL* 4.5 15.9 - - + -
149A TRP* 5.7 1.1 - + + -
150A LYS 3.6 0.9 - - - -
151A VAL* 3.6 35.0 - - + -
180A LEU* 4.8 2.9 - - + -
182A LEU* 3.9 10.6 - - + +
186A ASP 3.8 0.7 + - - -
187A TYR* 2.9 55.7 + + - -
190A HIS* 3.4 29.3 - - + +
191A LYS 3.6 15.7 - - - -
192A VAL* 1.3 72.7 - - - +
194A ALA* 1.3 60.8 + - - +
209A SER* 3.0 5.0 - - - -
210A PHE* 2.9 72.5 + + + +
212A ARG* 4.1 3.4 - - + -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.2 1.5 - - - +
148A GLN 3.5 0.7 - - - +
149A TRP* 3.4 13.5 - - - -
150A LYS* 2.7 55.8 + - + +
192A VAL* 4.9 6.7 - - + -
193A TYR* 1.3 76.7 - - - +
195A CYS* 1.3 60.5 + - - +
196A GLU* 4.0 0.7 - - + -
207A THR* 4.0 13.9 - - + -
208A LYS 3.5 4.0 - - - +
209A SER* 3.7 14.8 - - - -
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Residues in contact with CYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A VAL* 4.6 0.9 - - - +
118A ILE* 4.1 11.0 - - + +
135A CYS* 2.0 53.8 - - + -
147A VAL* 3.8 19.7 - - - -
148A GLN 3.6 2.5 - - - -
149A TRP* 4.3 6.3 - - + -
194A ALA* 1.3 72.5 - - - +
196A GLU* 1.3 60.8 + - - +
197A VAL* 4.0 9.6 + - - +
206A VAL 3.5 1.9 - - - +
207A THR* 3.3 3.0 - - - -
208A LYS* 2.8 39.2 + - + +
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS 3.4 4.5 - - - +
147A VAL* 3.5 0.9 - - - -
148A GLN* 2.8 68.9 + - + +
150A LYS* 3.4 30.9 + - + +
194A ALA 5.5 0.4 - - - +
195A CYS* 1.3 72.9 - - - +
197A VAL* 1.3 65.6 + - - +
198A THR* 4.1 5.4 + - - -
205A PRO* 4.0 23.9 - - + +
206A VAL 3.3 3.8 - - - +
207A THR* 3.3 22.9 + - + +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PRO* 4.3 10.3 - - + -
116A VAL* 3.9 22.7 - - + -
137A LEU* 3.8 42.8 - - + -
146A LYS 3.3 7.2 - - - +
147A VAL* 4.5 2.2 - - + -
195A CYS* 4.0 9.0 - - - +
196A GLU* 1.3 77.8 - - - +
198A THR* 1.3 73.9 + - - +
199A HIS* 4.7 0.9 - - + -
202A LEU* 3.7 17.0 - - + +
205A PRO* 3.1 6.4 - - - +
206A VAL* 2.7 40.5 + - + +
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA* 3.8 3.3 - - - -
146A LYS* 3.0 49.4 + - + +
148A GLN* 4.9 4.2 + - - -
196A GLU* 4.1 7.1 + - - -
197A VAL* 1.3 76.8 - - - +
199A HIS* 1.3 68.8 + - - +
202A LEU* 4.9 0.2 - - - -
205A PRO* 3.7 24.9 - - + +
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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