Contacts of the strand formed by residues 205 - 213 (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 ASP 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.2 26.2 - - + +
196A TYR* 3.3 4.6 - - - -
197A ASP* 2.7 45.8 + - - +
199A ASP* 2.8 4.0 - - - +
203A ARG* 3.2 4.0 - - - +
204A ASN* 1.3 73.8 - - - +
206A ALA* 1.3 62.9 + - - +
302A CA 2.4 30.8 - - - -
303A CA 2.5 21.4 - - - -
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Residues in contact with ALA 206 (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* 3.7 15.9 - - - +
195A VAL 4.0 1.6 - - - +
196A TYR* 3.7 26.1 - - + +
204A ASN 4.1 1.4 + - - -
205A ASP* 1.3 71.6 - - - +
207A ILE* 1.3 64.1 + - - +
208A GLY* 4.8 2.7 - - - +
232A ALA* 6.1 5.2 - - + -
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Residues in contact with ILE 207 (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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109A LEU* 3.7 43.5 - - - +
135A LEU* 4.3 11.7 - - + -
136A ALA* 3.9 24.2 - - + +
138A LEU* 3.8 14.6 - - + +
144A SER* 3.7 29.8 - - - +
146A PRO* 4.6 1.3 - - + -
195A VAL* 2.9 26.7 + - + +
196A TYR 3.9 15.7 - - - +
197A ASP* 3.9 14.6 - - + +
206A ALA* 1.3 76.5 - - - +
208A GLY* 1.3 60.3 + - - +
229A LEU* 4.0 6.5 - - + -
231A ALA* 5.7 0.3 - - - -
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Residues in contact with GLY 208 (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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109A LEU* 4.3 0.4 - - - -
194A ALA* 3.9 0.2 - - - -
195A VAL* 2.8 30.6 + - - +
206A ALA* 3.8 3.9 - - - +
207A ILE* 1.3 82.1 - - - +
209A GLU* 1.3 62.4 + - - +
229A LEU* 3.7 16.7 - - - +
230A GLN 3.3 13.0 - - - -
231A ALA* 5.0 2.7 - - - -
232A ALA 5.5 1.3 - - - -
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Residues in contact with GLU 209 (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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151A TYR* 4.8 2.4 + - - -
192A VAL* 4.1 9.3 - - + +
193A MET 3.4 11.7 - - - +
194A ALA* 3.7 20.8 - - + +
196A TYR* 5.5 0.9 + - - -
208A GLY* 1.3 75.9 - - - +
210A VAL* 1.3 64.5 + - - +
211A ARG* 2.7 46.5 + - + +
229A LEU* 3.5 2.3 - - - -
230A GLN* 2.8 47.4 + - + +
231A ALA 4.6 1.6 - - - +
232A ALA* 3.9 22.9 - - + +
233A PRO* 3.3 9.5 - - - +
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Residues in contact with VAL 210 (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* 4.1 13.0 - - + -
114A TYR* 4.4 1.3 - - + -
191A LEU 3.6 1.4 - - - +
192A VAL* 3.6 2.8 - - - +
193A MET* 2.9 58.9 + - + +
209A GLU* 1.3 76.3 - - - +
211A ARG* 1.3 64.3 + - - +
212A VAL* 4.0 11.4 + - + -
227A ARG* 3.6 38.4 - - + +
228A GLU 3.7 19.7 - - - +
229A LEU* 4.0 15.3 - - + -
230A GLN* 5.8 0.4 - - - -
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Residues in contact with ARG 211 (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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151A TYR* 4.2 14.3 + - - -
153A LEU* 3.4 23.8 - - - +
190A VAL* 4.3 12.7 - - + +
191A LEU 3.3 4.9 - - - +
192A VAL* 4.0 16.9 - - + +
209A GLU* 2.7 36.8 + - + +
210A VAL* 1.3 78.1 - - - +
212A VAL* 1.3 61.9 + - - +
213A PRO* 3.5 9.9 - - + +
227A ARG* 3.7 11.4 + - - -
230A GLN* 6.1 1.6 - - - +
233A PRO* 3.6 28.8 - - - +
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Residues in contact with VAL 212 (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 TYR* 3.7 26.5 - - + +
116A LEU* 4.6 3.8 - - + -
190A VAL* 4.2 1.8 - - - -
191A LEU* 2.8 45.0 + - + +
193A MET* 3.8 26.2 - - + -
210A VAL* 4.0 6.1 - - + -
211A ARG* 1.3 77.7 - - - +
213A PRO* 1.3 68.8 - - - +
214A MET* 3.2 7.7 + - - +
216A SER* 4.0 4.9 - - - +
217A VAL* 3.5 32.3 - - + -
227A ARG* 4.0 9.6 - - - +
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Residues in contact with PRO 213 (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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187A GLY 5.9 0.2 - - - +
189A ARG 3.9 6.5 - - - +
190A VAL* 4.3 16.4 - - + -
211A ARG* 3.5 11.9 - - + +
212A VAL* 1.3 82.8 - - - +
214A MET* 1.3 53.3 + - - +
215A SER* 3.1 16.6 - - - +
216A SER* 2.5 52.0 + - - +
217A VAL 4.1 0.2 + - - -
227A ARG* 4.2 6.3 - - - +
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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