Contacts of the strand formed by residues 159 - 166 (chain D) in PDB entry 5ZRV
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 VAL 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D VAL 5.1 3.9 + - - -
98D VAL* 5.5 2.7 - - - +
99D ASP* 3.5 15.0 + - - +
100D TYR* 3.3 23.0 + - - -
158D ASP* 1.3 77.4 + - - +
160D ILE* 1.3 58.5 + - - +
320D ILE 3.3 10.8 - - - -
321D MET* 4.7 2.5 - - - +
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D TYR 3.9 10.1 - - - -
148D GLY* 6.1 4.9 - - - -
159D VAL* 1.3 74.8 - - - +
161D VAL* 1.3 60.1 + - - +
319D LEU* 3.5 3.5 - - - -
320D ILE* 2.8 36.6 + - - +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D TYR 3.9 7.4 + - - +
101D ILE* 4.1 7.3 - - - +
102D ILE* 2.8 28.8 + - - +
160D ILE* 1.3 74.3 - - - +
162D ALA* 1.3 58.8 + - - +
318D MET 3.8 11.9 - - - -
319D LEU* 4.7 0.4 - - - +
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE 3.3 5.2 - - - -
144D ALA* 5.3 14.8 - - - +
145D MET* 5.5 3.1 - - - +
160D ILE 4.1 1.2 + - - -
161D VAL* 1.3 74.8 - - - +
163D GLY* 1.3 58.5 + - - +
317D ALA* 3.3 2.5 - - - -
318D MET* 3.0 29.3 + - - -
319D LEU* 5.3 0.4 - - - +
435D CYS* 6.1 0.9 - - - -
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Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE 3.3 7.9 + - - -
103D PHE* 3.2 6.7 - - - -
104D GLY* 3.0 23.7 + - - -
141D ALA* 4.7 9.8 - - - -
144D ALA* 5.9 2.6 - - - +
162D ALA* 1.3 74.8 - - - +
164D GLY* 1.3 57.8 + - - -
316D SER 2.9 16.2 - - - -
317D ALA* 3.9 2.7 - - - -
435D CYS* 6.4 1.8 - - - -
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Residues in contact with GLY 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLY* 3.4 11.2 - - - -
141D ALA* 4.8 5.8 - - - +
163D GLY* 1.3 75.0 - - - -
165D VAL* 1.3 58.1 + - - -
314D GLY 4.1 0.7 - - - +
315D ALA* 3.1 4.7 - - - -
316D SER* 2.9 31.0 + - - +
431D GLY 3.8 14.4 - - - -
432D ALA* 4.2 14.2 + - - -
435D CYS* 6.3 1.6 - - - +
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Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO 5.1 7.0 - - - +
80D ALA* 5.7 9.9 - - - +
104D GLY 3.3 8.9 + - - +
105D THR* 3.9 18.8 - - - -
164D GLY* 1.3 74.3 - - - -
166D GLU* 1.3 59.3 + - - +
314D GLY 3.8 4.5 - - - -
315D ALA* 4.1 4.9 - - - +
431D GLY 4.2 3.9 + - - -
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO* 5.6 4.5 - - - -
105D THR* 5.9 0.4 - - - +
106D VAL 6.1 1.3 - - - +
165D VAL* 1.3 75.0 - - - +
167D LEU* 1.3 56.9 + - - +
168D MET 4.2 0.7 - - - -
312D THR 5.6 0.7 - - - -
313D ASP* 3.6 1.8 - - - -
314D GLY 3.0 36.1 + - - +
431D GLY 5.8 4.2 - - - +
432D ALA* 5.9 0.6 - - - +
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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