Contacts of the strand formed by residues 97 - 101 (chain D) in PDB entry 5ZR1
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 SER 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D SER 3.7 0.6 + - - -
96D HIS* 1.3 76.5 - - - +
98D VAL* 1.3 65.8 + - - +
235D PHE* 4.2 8.4 - - - -
238D VAL* 3.7 26.9 - - - +
247D ILE* 3.6 22.7 - - - +
268D PHE* 3.4 24.2 - - - -
269D SER* 2.4 36.8 + - - -
271D ARG* 4.3 3.5 - - - +
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Residues in contact with VAL 98 (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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85D ILE* 3.9 32.3 - - + -
96D HIS* 5.4 1.3 - - + +
97D SER* 1.3 78.3 - - - +
99D ILE* 1.3 73.2 + - - +
100D LEU* 4.2 0.4 - - + -
246D CYS* 5.6 0.2 - - - -
247D ILE* 3.0 20.9 + - - +
248D PHE* 3.4 34.1 - - + -
249D GLY 3.2 12.5 + - - -
268D PHE* 4.0 2.8 - - - -
271D ARG* 3.3 35.0 - - + +
273D ILE* 4.2 13.9 - - + -
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Residues in contact with ILE 99 (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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98D VAL* 1.3 77.2 - - - +
100D LEU* 1.3 68.3 + - - +
101D VAL 3.9 0.2 + - - -
219D ILE* 4.4 24.2 - - + -
235D PHE* 5.0 2.9 - - + -
249D GLY 3.3 15.9 - - - +
251D THR* 3.8 19.3 - - + -
256D ILE* 4.2 19.7 - - + -
257D LEU* 5.2 0.7 - - + -
260D LEU* 4.8 11.7 - - + -
268D PHE* 3.6 34.1 - - + -
271D ARG 3.2 6.5 + - - -
272D VAL* 3.5 19.1 - - + +
273D ILE* 3.1 26.3 + - - +
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Residues in contact with LEU 100 (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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82D ILE* 3.8 23.6 - - + -
98D VAL* 4.2 1.5 + - + -
99D ILE* 1.3 74.1 - - - +
101D VAL* 1.3 60.5 + - - +
108D LYS* 4.1 25.1 - - + +
112D LEU* 3.7 40.6 - - + -
248D PHE* 4.0 15.0 - - + -
249D GLY 2.7 21.8 + - - +
250D CYS* 3.4 10.6 - - - -
251D THR 3.0 16.8 + - - +
273D ILE* 3.7 34.1 - - + -
275D MET* 4.4 7.6 - - - -
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Residues in contact with VAL 101 (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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99D ILE* 4.7 0.2 - - + -
100D LEU* 1.3 76.9 - - - +
102D GLY* 1.3 60.0 + - - +
251D THR* 3.4 15.7 - - + +
252D THR 3.9 11.9 - - - +
253D LYS 3.3 26.5 - - - +
254D LEU* 4.5 5.8 - - + -
256D ILE* 5.1 1.3 - - + -
272D VAL* 3.6 23.1 - - + -
273D ILE 3.2 16.0 + - - +
274D TYR* 3.4 30.7 - - + +
275D MET* 2.8 30.4 + - - +
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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