Contacts of the strand formed by residues 173 - 178 (chain A) in PDB entry 6XAV
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 ARG 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLY 3.7 3.8 + - - +
172A GLN* 1.3 76.3 - - - +
174A GLY* 1.3 57.9 + - - +
301A PHE* 3.3 51.8 - - + +
302A GLY* 3.8 14.8 + - - -
304A ALA* 2.9 30.3 + - + +
305A ARG* 4.9 0.8 - - - +
315A ILE 4.1 4.0 - - - -
338A THR* 3.7 17.8 + - - +
339A GLY* 3.3 3.6 - - - -
340A ASN* 2.9 50.5 + - - +
212B ARG* 3.3 26.3 - - - +
214B GLU* 2.6 33.7 + - - +
232B PHE* 5.7 2.2 - - - -
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Residues in contact with GLY 174 (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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172A GLN* 3.9 1.8 - - - +
173A ARG* 1.3 75.5 - - - +
175A LEU* 1.3 63.4 + - - +
176A ILE* 5.7 0.7 - - - -
301A PHE* 3.1 17.8 - - - -
315A ILE 3.7 6.2 + - - +
316A ILE* 4.4 13.4 - - - +
317A ALA 3.6 14.6 + - - -
339A GLY* 5.0 0.7 - - - -
340A ASN 4.8 0.2 - - - -
341A MET* 3.2 26.9 - - - -
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Residues in contact with LEU 175 (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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174A GLY* 1.3 73.8 - - - +
176A ILE* 1.3 65.5 + - - +
177A VAL* 3.5 15.8 + - + -
267A ILE* 3.7 26.2 - - + -
301A PHE* 3.5 26.9 - - + -
317A ALA* 3.4 15.0 - - + +
319A ALA* 4.8 12.1 - - + -
332A TYR* 5.5 4.5 - - + +
335A PHE* 3.3 40.8 - - + +
336A LYS* 4.6 4.3 - - - +
339A GLY* 5.4 2.9 - - - +
341A MET* 2.8 15.5 + - - +
342A GLU* 3.6 7.7 - - + +
343A LEU 3.1 22.9 + - - -
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Residues in contact with ILE 176 (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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162A LEU* 6.0 0.2 - - + -
168A ILE* 6.2 3.4 - - + -
174A GLY 5.7 0.2 - - - -
175A LEU* 1.3 72.5 - - - +
177A VAL* 1.3 64.5 + - - +
178A ALA* 3.5 4.2 + - + +
184A LYS* 5.6 3.8 - - + -
187A LEU* 4.2 25.1 - - + -
188A LEU* 6.2 0.7 - - + -
191A ILE* 5.3 4.3 - - + -
316A ILE* 3.7 26.5 - - + -
317A ALA 2.6 21.6 + - - +
318A THR* 3.3 21.7 - - + +
319A ALA 2.9 24.2 + - - +
341A MET* 5.9 6.3 - - + -
343A LEU* 3.7 40.4 - - + +
345A LEU* 4.9 10.5 - - + -
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Residues in contact with VAL 177 (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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175A LEU* 3.5 21.0 + - + +
176A ILE* 1.3 71.6 - - - +
178A ALA* 1.3 64.8 + - - +
179A PRO* 4.8 0.2 - - - -
319A ALA* 3.9 7.0 - - + +
321A ILE* 3.7 28.9 - - + -
332A TYR* 3.6 35.7 - - + -
342A GLU* 4.9 7.4 - - + -
343A LEU 2.9 19.6 + - - +
344A HIS* 3.2 34.7 - - + +
345A LEU 3.0 15.4 + - - -
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Residues in contact with ALA 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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176A ILE* 4.4 4.9 - - + +
177A VAL* 1.3 79.1 - - - +
179A PRO* 1.3 73.7 - - + +
182A ALA* 4.2 1.6 - - + -
184A LYS* 3.7 23.9 - - + +
319A ALA 3.3 19.0 + - - +
320A LEU* 3.8 10.4 - - - +
321A ILE* 3.9 6.8 + - - -
345A LEU* 3.6 30.7 - - + -
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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
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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