Contacts of the strand formed by residues 173 - 177 (chain A) in PDB entry 1ECX
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 LEU 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A VAL* 4.2 8.7 - - + -
85A PHE* 3.9 29.4 - - + -
141A PHE 2.9 18.9 + - - +
142A LEU* 3.2 11.8 - - + +
143A VAL 2.8 26.3 + - - -
171A GLU 4.3 8.1 - - - +
172A THR* 1.3 75.1 - - - +
174A VAL* 1.3 61.1 + - - +
195A ASP* 3.1 26.7 - - + +
196A TYR* 3.9 17.9 - - + +
219A VAL* 3.8 23.6 - - + -
220A PRO* 4.0 11.0 - - + -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 3.4 15.3 - - + +
145A ILE* 4.6 9.4 - - + -
161A VAL* 5.7 2.9 - - + -
162A THR* 4.3 21.3 - - + +
165A VAL* 4.2 28.3 - - + -
172A THR 4.4 3.4 - - - +
173A LEU* 1.3 79.8 - - - +
175A HIS* 1.3 64.1 + - - +
176A VAL* 4.2 11.4 - - + -
193A GLU 5.2 0.7 - - - +
194A VAL* 4.0 25.2 - - + +
195A ASP* 2.8 39.9 + - - +
196A TYR* 3.0 8.5 + - - +
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Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.2 24.5 - - + +
77A ILE* 3.9 15.1 - - + +
78A LEU* 4.4 5.8 - - + +
102A VAL* 5.0 0.9 - - + -
142A LEU* 4.2 11.8 - - + +
143A VAL 2.9 9.0 + - - +
144A SER* 2.9 27.4 + - - +
145A ILE* 3.0 26.3 + - - +
173A LEU 4.3 0.2 - - - -
174A VAL* 1.3 74.1 - - - +
176A VAL* 1.3 73.4 + - - +
177A ASP* 4.0 18.2 - - + -
196A TYR* 3.2 39.7 - - + -
197A ALA 3.9 1.1 - - - -
198A SER* 3.0 27.4 + - - -
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.1 19.5 - - + +
146A MET 4.4 0.4 - - - -
147A ALA* 3.9 27.4 - - + +
158A VAL* 4.0 17.5 - - + -
174A VAL* 4.2 2.9 - - + -
175A HIS* 1.3 82.1 - - - +
177A ASP* 1.3 65.4 + - - +
178A ALA* 3.0 13.7 + - + +
187A PHE* 4.4 12.3 - - + -
192A LEU* 5.1 0.9 - - + -
194A VAL* 3.9 29.6 - - + -
196A TYR 2.7 12.8 + - - +
197A ALA* 3.2 5.3 - - + +
198A SER 3.1 19.8 + - - -
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.9 14.8 - - + +
98A GLU* 4.5 6.6 - - - +
99A HIS* 4.2 6.8 - - - +
102A VAL* 4.5 4.8 - - + +
145A ILE 3.0 8.6 + - - +
146A MET* 3.5 16.9 - - + +
147A ALA* 3.1 19.2 + - - +
148A ALA 4.7 1.7 + - - +
175A HIS* 4.0 16.4 - - + -
176A VAL* 1.3 69.9 - - - +
178A ALA* 1.3 55.4 + - - +
179A VAL* 3.1 30.7 + - - +
180A GLN 5.1 0.7 + - - -
198A SER* 4.2 4.2 - - - +
500A PLP 2.6 37.7 + - - +
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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
------------------------------------------------------------
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