Contacts of the strand formed by residues 173 - 177 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL* 4.3 6.3 - - + -
85B PHE* 4.1 18.2 - - + -
141B PHE 2.8 15.4 + - - +
142B LEU* 3.3 12.9 - - + +
143B VAL 2.8 26.2 + - - -
171B GLU 4.1 8.3 - - - +
172B THR* 1.3 80.5 - - - +
174B VAL* 1.3 63.3 + - - +
195B ASP* 3.1 30.3 - - + +
196B TYR* 3.5 25.6 - - + +
219B VAL* 4.3 12.8 - - + -
220B PRO* 3.6 21.1 - - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.4 15.0 - - + +
145B ILE* 4.5 10.1 - - + -
161B VAL* 5.5 2.0 - - + -
162B THR* 4.5 26.0 - - + +
165B VAL* 4.3 27.8 - - + -
172B THR 4.7 3.1 - - - +
173B LEU* 1.3 79.4 - - - +
175B HIS* 1.3 63.8 + - - +
176B VAL* 4.1 19.7 - - + -
193B GLU 5.6 0.7 - - - +
194B VAL* 4.0 10.4 - - + +
195B ASP* 2.9 40.7 + - - +
196B TYR* 3.0 9.9 + - - +
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Residues in contact with HIS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.1 25.1 - - + +
77B ILE* 4.2 16.4 - - + +
78B LEU* 4.2 8.4 - - + +
102B VAL* 4.9 1.3 - - + -
142B LEU* 4.3 12.0 - - + +
143B VAL 2.9 8.7 + - - +
144B SER* 2.9 28.7 + - - +
145B ILE* 3.0 27.9 + - - +
174B VAL* 1.3 73.8 - - - +
176B VAL* 1.3 70.9 + - - +
177B ASP* 4.0 17.5 - - + -
196B TYR* 3.2 34.1 - - + -
197B ALA 4.0 1.1 - - - -
198B SER* 2.9 29.8 + - - -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.1 11.7 - - + +
147B ALA* 4.0 26.5 - - + +
158B VAL* 4.0 16.8 - - + -
174B VAL* 4.1 7.9 - - + -
175B HIS* 1.3 82.1 - - - +
177B ASP* 1.3 62.9 + - - +
178B ALA 2.9 9.7 + - - +
187B PHE* 4.2 19.1 - - + -
194B VAL* 3.7 34.3 - - + -
196B TYR 2.7 12.6 + - - +
197B ALA* 3.2 7.0 - - + +
198B SER 3.1 18.2 + - - -
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.7 14.6 - - + +
98B GLU* 4.4 5.6 - - - +
99B HIS* 4.2 7.3 - - - +
102B VAL* 4.2 6.5 - - + +
144B SER* 5.8 0.2 - - - +
145B ILE 3.0 9.0 + - - +
146B MET* 3.4 17.4 - - + +
147B ALA* 3.0 21.5 + - - +
148B ALA 4.6 2.6 + - - +
175B HIS* 4.0 18.0 - - + -
176B VAL* 1.3 67.7 - - - +
178B ALA* 1.3 57.8 + - - +
179B VAL* 3.0 28.2 + - - +
180B GLN 5.2 0.3 + - - -
198B SER* 4.4 4.0 - - - -
501B PLP 2.6 35.1 + - - +
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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
------------------------------------------------------------
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