Contacts of the strand formed by residues 190 - 197 (chain A) in PDB entry 5H4Y
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LEU* 4.0 1.8 - - - -
153A LEU* 2.8 50.8 + - + +
188A GLY 5.0 4.0 - - - +
189A ARG* 1.3 77.8 - - - +
191A LEU* 1.3 72.8 + - - +
192A VAL* 3.5 7.4 + - + -
211A ARG* 4.3 20.9 - - + +
212A VAL 3.6 12.8 - - - +
213A PRO* 4.3 14.6 - - + -
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Residues in contact with LEU 191 (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 LEU* 3.5 32.1 - - + -
125A LEU* 5.2 0.4 - - + -
127A VAL* 3.9 20.4 - - + -
150A VAL* 3.8 24.5 - - + -
151A TYR 3.7 15.0 - - - +
152A LEU* 3.7 18.1 - - + +
179A PHE* 4.2 7.0 - - + -
189A ARG 4.2 0.2 - - - -
190A VAL* 1.3 73.5 - - - +
192A VAL* 1.3 62.1 + - - +
193A MET* 3.9 26.5 - - + -
210A VAL 3.6 1.0 - - - +
211A ARG* 3.3 4.7 - - - -
212A VAL* 2.8 48.7 + - + +
214A MET* 4.1 8.0 - - - +
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Residues in contact with VAL 192 (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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149A ARG 3.5 1.2 - - - +
150A VAL* 3.3 6.6 - - - +
151A TYR* 2.9 68.2 + - + +
153A LEU* 3.6 33.9 - - + -
190A VAL* 4.0 1.8 - - + +
191A LEU* 1.3 78.9 - - - +
193A MET* 1.3 65.0 + - - +
194A ALA* 4.2 8.3 - - + +
209A GLU* 4.1 24.2 - - - +
210A VAL 3.6 4.7 - - - +
211A ARG* 4.0 17.3 - - + +
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Residues in contact with MET 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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112A LEU* 3.7 16.2 - - + -
114A TYR* 3.7 35.4 - - + -
127A VAL* 4.1 2.5 - - - -
129A ILE* 3.6 28.3 - - + -
148A VAL* 3.9 9.0 - - + -
149A ARG 3.5 4.5 - - - -
150A VAL* 4.1 11.0 - - + -
191A LEU* 3.9 19.7 - - + -
192A VAL* 1.3 74.8 - - - +
194A ALA* 1.3 61.2 + - - +
195A VAL* 3.8 5.7 + - - +
209A GLU* 3.4 2.6 - - - -
210A VAL* 2.9 62.2 + - + +
212A VAL* 3.8 16.6 - - + -
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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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148A VAL* 3.4 2.3 - - - -
149A ARG* 2.8 44.3 + - + +
151A TYR* 4.9 6.3 - - + +
192A VAL* 3.8 7.8 - - + -
193A MET* 1.3 70.9 - - - +
195A VAL* 1.3 60.8 + - - +
196A TYR* 3.4 31.0 - - + +
208A GLY 4.7 0.4 - - - +
209A GLU* 3.7 25.6 - - + +
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Residues in contact with VAL 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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112A LEU* 4.5 12.8 - - + -
132A ALA* 5.6 0.9 - - + -
135A LEU* 4.0 22.2 - - + -
146A PRO* 4.4 4.7 - - + -
147A TYR 3.4 9.9 - - - +
148A VAL* 4.1 19.7 - - + +
173A PHE* 5.2 1.1 - - + -
193A MET 4.3 7.0 - - - +
194A ALA* 1.3 74.1 - - - +
196A TYR* 1.3 65.3 + - - +
206A ALA* 3.9 1.6 - - - +
207A ILE* 2.9 42.6 + - + -
208A GLY 2.8 19.7 + - - +
229A LEU* 3.8 27.4 - - + -
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Residues in contact with TYR 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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145A ASP 3.7 0.2 - - - +
146A PRO* 3.2 6.9 - - - +
147A TYR* 2.8 69.9 + + + +
149A ARG* 4.2 32.1 + - + -
194A ALA* 3.4 36.8 - - + +
195A VAL* 1.3 75.8 - - - +
197A ASP* 1.3 61.1 + - - +
198A PHE 4.0 0.4 - - - -
204A ASN* 4.7 8.3 - - + -
205A ASP 3.3 16.6 - - - -
206A ALA* 3.7 24.6 - - + +
207A ILE* 3.9 6.6 - - - +
209A GLU* 5.5 1.0 + - - -
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Residues in contact with ASP 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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138A LEU* 3.3 24.6 - - + +
139A ASP* 3.0 2.8 - - - +
144A SER* 3.5 6.4 - - - +
145A ASP 2.8 23.6 + - - -
196A TYR* 1.3 72.1 - - - +
198A PHE* 1.3 62.3 + - - +
199A ASP* 3.2 0.9 - - - +
204A ASN* 3.2 6.5 - - - +
205A ASP* 2.7 43.2 + - + +
207A ILE* 4.0 11.0 - - + -
301A CA 2.4 24.1 - - - -
302A CA 2.3 30.8 - - - -
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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