Contacts of the strand formed by residues 177 - 182 (chain A) in PDB entry 3EVG
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 GLN 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.4 7.3 - - + +
72A THR* 2.5 46.7 - - - +
74A GLU* 3.3 26.7 - - - +
141A ASP 2.9 6.1 + - - -
142A THR* 2.9 21.2 - - + -
143A LEU 2.7 32.1 + - - -
175A ASN 3.3 4.4 + - - +
176A THR* 1.3 77.6 - - - +
178A PHE* 1.3 54.0 + - - +
222A SER* 3.6 2.7 + - - -
223A ASN* 3.0 35.2 + - - +
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Residues in contact with PHE 178 (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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71A VAL* 3.0 21.3 - - - +
143A LEU 3.1 14.1 - - - +
172A LEU* 3.8 28.3 - - + -
176A THR* 3.4 22.0 - - - -
177A GLN* 1.3 74.1 - - - +
179A CYS* 1.3 61.0 + - - +
180A ILE* 4.4 7.9 - - + -
201A TYR* 3.7 30.1 - + + -
202A GLY 4.0 1.8 - - - -
220A TRP* 3.4 55.0 - + - -
221A VAL* 3.4 2.5 - - - -
222A SER* 3.1 45.4 + - - -
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.7 5.8 - - + -
65A PHE* 3.7 33.2 - - - -
71A VAL* 3.3 20.0 - - + -
87A TRP* 3.6 20.4 - - - -
143A LEU 3.2 4.6 + - - -
144A LEU* 3.5 18.4 - - + +
145A CYS 3.0 24.1 + - - +
178A PHE* 1.3 73.2 - - - +
180A ILE* 1.3 60.4 + - - +
219A TYR* 4.0 4.0 - - - -
220A TRP 3.4 4.5 - - - -
221A VAL* 3.9 10.5 - - - -
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Residues in contact with ILE 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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143A LEU* 4.3 18.8 - - + +
145A CYS* 3.3 16.4 - - + +
164A VAL* 4.1 7.4 - - + -
165A LEU* 5.0 8.1 - - + -
168A VAL* 3.3 52.3 - - + -
172A LEU* 4.8 2.2 - - + -
178A PHE* 4.4 10.5 - - + -
179A CYS* 1.3 80.1 - - - +
181A LYS* 1.3 75.1 + - - +
182A VAL* 3.5 0.5 + - - +
219A TYR* 3.8 3.4 - - - -
220A TRP* 2.6 60.2 + - + +
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Residues in contact with LYS 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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61A LYS* 5.8 0.2 - - - +
145A CYS 2.8 13.8 + - - +
146A ASP* 3.2 37.3 + - - +
147A ILE 4.0 6.7 - - - +
148A GLY* 3.0 30.4 + - - -
161A THR* 5.6 0.3 - - - +
164A VAL* 4.2 12.3 - - - +
165A LEU* 5.3 0.7 - - - +
180A ILE* 1.3 86.2 - - - +
182A VAL* 1.3 64.1 + - - +
183A LEU* 3.8 24.8 + - - +
217A GLU* 3.2 26.4 + - + +
218A MET 3.9 1.1 - - - +
219A TYR* 3.3 31.1 + - + +
901A SAH 6.3 0.4 - - - -
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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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161A THR* 3.8 23.6 - - + -
165A LEU* 4.2 10.1 - - + -
180A ILE* 3.8 9.9 - - + +
181A LYS* 1.3 81.1 - - - +
183A LEU* 1.3 64.3 + - - +
185A PRO* 3.6 30.1 - - + +
190A VAL* 4.0 7.9 - - + -
194A MET* 4.1 13.5 - - + -
205A LEU* 3.7 25.4 - - + -
218A MET 2.7 31.1 + - - +
220A TRP* 4.1 7.9 - - + -
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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