Contacts of the strand formed by residues 238 - 245 (chain A) in PDB entry 4Z1H
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LYS* 4.3 12.3 - - + -
88A HIS 3.1 16.4 - - - +
89A GLU* 3.6 28.5 - - + +
90A PHE* 4.7 0.7 - - - -
233A SER* 3.5 14.4 + - - -
234A ASP* 3.6 5.5 - - - +
236A SER* 3.1 19.8 + - - +
237A GLY* 1.3 85.7 - - - +
239A PHE* 1.3 70.3 + - - +
240A GLU* 4.9 5.1 - - + +
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Residues in contact with PHE 239 (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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88A HIS* 2.9 72.6 + + + +
89A GLU 4.6 6.1 - - - -
90A PHE* 3.7 35.9 - + + -
168A LEU 4.5 2.5 - - - -
169A VAL* 3.9 21.5 - - + -
231A TRP* 3.3 41.1 - + + -
232A LEU 3.1 16.2 - - - +
233A SER* 3.9 4.5 - - - +
238A VAL* 1.3 76.3 - - - +
240A GLU* 1.3 64.6 + - - +
241A ILE* 4.1 13.9 - - + -
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Residues in contact with GLU 240 (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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85A THR* 2.4 40.0 + - + +
86A SER 3.7 4.7 - - - -
87A LYS* 2.6 29.8 + - + +
231A TRP* 3.5 3.6 - - - -
232A LEU* 2.9 57.6 + - + +
238A VAL* 5.3 3.6 - - + +
239A PHE* 1.3 78.8 - - - +
241A ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 241 (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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84A SER 4.3 0.2 - - - +
85A THR* 3.1 5.7 - - - -
86A SER* 2.9 53.4 + - - +
88A HIS* 4.5 10.1 - - + +
165A GLN* 4.9 18.4 - - + +
168A LEU* 4.0 25.1 - - + -
169A VAL* 3.7 28.5 - - + +
229A TYR* 5.4 3.1 - - + -
230A GLN* 3.4 14.4 - - - +
231A TRP* 4.0 15.3 - - + -
239A PHE* 4.1 10.5 - - + -
240A GLU* 1.3 76.0 - - - +
242A ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 242 (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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81A VAL* 3.7 28.3 - - + -
84A SER 4.2 9.6 - - - +
85A THR* 3.8 15.5 - - + -
229A TYR* 3.2 15.5 - - - +
230A GLN* 2.9 37.7 + - + +
241A ILE* 1.3 80.5 - - - +
243A GLU* 1.3 59.7 + - - +
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Residues in contact with GLU 243 (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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81A VAL* 3.8 18.9 - - - +
82A GLN* 4.4 4.0 + - - +
83A GLY 5.2 1.7 + - - -
84A SER 5.5 0.2 + - - -
227A LEU* 3.5 37.8 - - + +
228A GLY 3.7 9.2 - - - +
229A TYR* 3.6 20.2 + - + -
242A ALA* 1.3 73.3 - - - +
244A ALA* 1.3 68.0 + - - +
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Residues in contact with ALA 244 (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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80A SER 3.4 14.1 - - - +
81A VAL* 4.0 12.3 - - + -
218A TYR* 4.3 5.6 - - + -
227A LEU* 5.6 1.0 - - - +
228A GLY* 2.9 25.8 + - - +
229A TYR 4.2 0.9 - - - -
230A GLN* 4.0 18.4 - - + +
242A ALA 3.7 0.8 + - - -
243A GLU* 1.3 83.0 - - - +
245A SER* 1.3 63.0 + - - +
247A VAL* 3.8 20.9 - - + -
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Residues in contact with SER 245 (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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78A THR 3.5 0.7 - - - +
79A GLU* 3.2 2.6 - - - -
80A SER* 2.8 50.8 + - - -
82A GLN* 5.6 3.8 + - - +
244A ALA* 1.3 76.8 - - - +
246A GLY* 1.3 62.1 + - - +
247A VAL* 3.3 2.9 - - - +
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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