Contacts of the strand formed by residues 179 - 184 (chain A) in PDB entry 1ESD
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 ALA 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A THR* 3.4 10.9 + - + +
97A GLN 3.4 13.0 - - - -
98A LEU 4.2 2.2 - - - +
99A THR* 4.6 8.3 - - + -
172A ILE* 4.6 4.9 - - + -
173A GLY* 6.2 0.2 - - - -
176A ALA* 2.9 38.7 + - + +
177A PRO 4.8 2.6 - - - +
178A ASP* 1.3 79.5 - - - +
180A LYS* 1.3 66.3 + - - +
181A ARG* 3.9 13.9 + - - +
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Residues in contact with LYS 180 (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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97A GLN* 3.0 17.9 + - - +
98A LEU* 3.5 15.2 - - + +
99A THR* 2.8 28.2 + - - +
178A ASP 4.2 11.4 - - - -
179A ALA* 1.3 74.9 - - - +
181A ARG* 1.3 58.0 + - - +
182A VAL* 5.3 0.9 - - + -
241A ASP* 5.5 2.0 - - - +
303A ILE* 4.3 34.1 + - + -
304A LEU* 4.9 11.2 - - + +
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Residues in contact with ARG 181 (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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99A THR* 3.6 6.7 - - - +
169A LEU* 2.3 45.9 + - + +
170A ASP* 4.6 2.8 + - - +
172A ILE* 3.2 39.3 - - + -
173A GLY* 3.7 17.5 - - - +
179A ALA 3.9 11.2 + - - +
180A LYS* 1.3 73.5 - - - +
182A VAL* 1.3 58.6 - - - +
183A LEU 4.1 0.4 - - - -
238A GLY 2.6 28.9 + - - -
239A GLY* 3.9 16.1 + - - -
240A ALA* 3.3 16.2 - - + +
241A ASP* 2.8 34.7 + - - +
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Residues in contact with VAL 182 (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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11A PHE* 4.4 5.1 - - - -
98A LEU* 4.1 13.2 - - + -
99A THR 2.9 15.0 + - - +
100A VAL* 3.4 29.2 - - + -
101A GLY 3.3 23.9 + - - +
180A LYS 4.6 0.4 - - - +
181A ARG* 1.3 76.5 - - - +
183A LEU* 1.3 62.2 + - - +
184A VAL* 4.6 0.7 - - + -
241A ASP 3.4 6.3 - - - +
243A VAL* 3.6 31.0 - - + -
296A VAL* 5.7 1.6 - - + -
299A LYS* 4.2 9.2 - - + -
300A ILE* 5.2 6.7 - - + -
303A ILE* 3.9 22.0 - - + -
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Residues in contact with LEU 183 (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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11A PHE* 5.0 4.0 - - + -
101A GLY 3.5 11.7 - - - +
103A LEU 4.4 12.8 - - - +
165A LEU* 4.5 10.5 - - + -
168A LEU* 4.2 23.1 - - + -
169A LEU* 4.8 11.9 - - + -
181A ARG 4.1 0.6 - - - -
182A VAL* 1.3 75.1 - - - +
184A VAL* 1.3 61.1 - - - +
231A MET* 3.6 53.6 - - + +
234A ALA* 4.6 6.3 - - + -
235A ALA* 4.2 12.3 - - + +
240A ALA* 4.9 5.4 - - + -
241A ASP 2.9 10.1 + - - +
242A PHE* 3.2 13.3 - - + -
243A VAL* 3.0 23.2 + - - +
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Residues in contact with VAL 184 (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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41A TYR* 3.2 34.3 - - + +
100A VAL* 3.7 25.8 - - + -
101A GLY 3.0 13.3 + - - +
102A SER* 3.2 23.4 - - - -
182A VAL* 4.5 5.8 - - + +
183A LEU* 1.3 72.8 - - - +
185A GLY* 1.3 74.9 + - - +
231A MET* 3.4 11.3 - - - +
243A VAL* 3.9 7.0 - - + -
245A LEU* 3.6 19.5 - - + -
296A VAL* 3.8 22.4 - - + -
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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