Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 1GZH
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 ILE 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 4.2 12.1 - - + -
162A ILE 3.2 11.2 - - - +
163A TYR* 3.5 26.2 - - + -
164A LYS* 4.1 1.6 - - - +
173A VAL* 4.1 9.2 - - + -
194A LEU* 4.0 15.3 - - + -
236A TYR* 4.2 13.2 - - + -
240A SER* 5.5 1.1 + - - +
246A MET* 3.5 37.2 - - + -
250A PRO* 1.3 74.5 - - - +
252A LEU* 1.3 65.0 + - - +
253A THR* 4.7 1.6 - - - +
271A GLU* 3.4 11.4 - - - +
272A VAL* 3.1 53.5 + - + +
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Residues in contact with LEU 252 (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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100A GLN* 3.2 43.5 - - + +
160A MET 3.5 0.9 - - - +
161A ALA* 3.1 5.9 - - - -
162A ILE* 2.8 47.1 + - + -
164A LYS* 4.2 31.0 - - + +
251A ILE* 1.3 76.7 - - - +
253A THR* 1.3 63.3 + - - +
254A ILE* 3.6 5.4 - - + +
269A SER* 5.1 7.4 - - - +
270A PHE* 3.6 7.2 - - - +
271A GLU* 3.7 31.0 - - + +
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Residues in contact with THR 253 (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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159A ALA* 4.6 4.7 - - + -
160A MET 3.5 4.9 - - - +
161A ALA* 4.5 0.4 - - - +
195A ILE* 4.1 15.8 - - + +
234A TYR* 5.7 2.0 - - + -
236A TYR* 2.6 35.6 + - - +
251A ILE* 4.7 1.7 - - - +
252A LEU* 1.3 73.9 + - - +
254A ILE* 1.3 61.9 + - - +
255A ILE* 3.7 20.1 + - + -
269A SER* 3.2 23.4 - - - -
270A PHE* 2.9 34.0 + - + -
272A VAL* 3.3 10.3 - - - +
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Residues in contact with ILE 254 (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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98A PRO* 5.9 2.2 - - + -
99A SER 4.0 14.8 - - - +
100A GLN* 4.2 8.3 - - + -
158A ARG 3.6 1.2 - - - +
159A ALA* 3.5 2.9 - - - -
160A MET* 2.7 46.6 + - + +
162A ILE* 3.2 44.2 - - + -
252A LEU* 3.6 8.3 - - + +
253A THR* 1.3 72.9 - - - +
255A ILE* 1.3 63.8 + - - +
256A THR* 3.9 11.7 + - + -
267A ARG* 3.8 30.1 - - + -
268A ASN 3.5 9.9 - - - +
269A SER* 4.2 10.1 - - - -
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Residues in contact with ILE 255 (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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109A PHE* 3.8 21.5 - - + -
111A LEU* 4.1 21.1 - - + -
143A VAL* 4.8 1.6 - - + -
145A LEU* 4.3 3.1 - - + -
157A VAL* 3.8 24.7 - - + -
158A ARG 3.3 1.8 - - - +
159A ALA* 3.8 10.8 - - + -
234A TYR* 3.7 29.2 - - + +
253A THR* 3.7 21.3 - - + -
254A ILE* 1.3 71.7 - - - +
256A THR* 1.3 64.1 + - - +
267A ARG* 3.3 2.8 - - - -
268A ASN 2.7 37.8 + - - +
270A PHE* 3.9 22.2 - - + -
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Residues in contact with THR 256 (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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109A PHE* 4.7 0.2 - - - -
156A ARG 3.6 1.0 - - - +
157A VAL* 3.4 5.7 - - - +
158A ARG* 2.9 54.2 + - - +
254A ILE* 3.9 9.4 + - + -
255A ILE* 1.3 83.2 - - - +
257A LEU* 1.3 61.5 + - - +
258A GLU* 3.8 9.8 + - - -
264A LEU* 4.1 11.4 - - + -
266A GLY 3.3 4.3 - - - +
267A ARG* 3.8 34.5 - - + +
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Residues in contact with LEU 257 (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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107A TYR* 4.9 7.0 - - + -
109A PHE* 4.0 44.6 - - + -
145A LEU* 4.7 0.7 - - + -
147A VAL* 4.5 4.3 - - + -
151A PRO* 3.9 26.5 - - + -
155A THR* 3.9 12.8 - - + -
156A ARG 3.5 2.0 - - - +
157A VAL* 3.9 26.7 - - + -
220A TYR* 4.2 12.1 - - + -
256A THR* 1.3 72.1 - - - +
258A GLU* 1.3 54.5 + - - +
264A LEU* 3.8 1.9 - - - +
265A LEU* 2.7 42.4 + - + +
266A GLY* 2.7 24.1 + - - +
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Residues in contact with GLU 258 (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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155A THR* 3.1 6.1 - - - +
156A ARG* 2.7 59.0 + - + +
158A ARG* 2.8 53.3 + - + +
217A VAL* 5.3 0.4 - - - -
256A THR* 3.8 12.0 + - - +
257A LEU* 1.3 75.2 - - - +
259A ASP* 1.3 62.0 + - - +
262A GLY* 3.5 29.1 - - - +
263A ASN 3.1 15.7 - - - +
264A LEU* 4.8 1.3 - - + +
265A LEU* 3.2 6.7 - - - +
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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