Contacts of the strand formed by residues 264 - 274 (chain C) 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 LEU 264 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C TYR* 3.2 39.1 + - + -
256C THR* 4.3 13.0 - - + -
257C LEU 4.0 2.2 - - - +
258C GLU* 4.7 1.8 - - + +
262C GLY 3.8 1.8 + - - -
263C ASN* 1.3 74.8 - - - +
265C LEU* 1.3 64.7 - - - +
266C GLY 3.5 23.8 - - - +
267C ARG* 3.4 40.2 - - + +
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 4.1 6.6 - - - -
104C GLN 4.2 1.0 - - - +
105C GLY* 3.5 22.5 - - - -
106C SER* 4.2 7.5 + - - +
107C TYR* 3.9 41.1 - - + +
109C PHE* 5.5 0.5 - - - +
152C PRO* 5.6 2.2 - - + -
155C THR* 3.7 19.3 - - + +
257C LEU* 2.7 15.3 + - + +
258C GLU* 3.2 10.1 - - - +
259C ASP* 3.2 37.7 - - + +
263C ASN* 3.7 8.5 - - + +
264C LEU* 1.3 80.9 - - - +
266C GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C TYR* 3.2 15.0 - - - -
104C GLN 4.5 3.1 - - - -
109C PHE* 3.7 15.0 - - - -
256C THR* 3.3 3.3 - - - -
257C LEU* 2.7 36.2 + - - +
264C LEU* 3.5 8.6 - - - +
265C LEU* 1.3 80.0 - - - +
267C ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C SER* 3.3 53.4 + - - +
100C GLN 4.3 1.8 - - - -
101C LYS* 3.0 31.6 + - - +
102C THR* 3.7 0.6 - - - -
103C TYR* 2.7 41.3 + - + +
109C PHE* 3.6 2.8 - - - -
254C ILE* 4.0 8.5 - - + -
255C ILE 3.3 7.2 - - - +
256C THR* 3.9 21.5 - - + +
264C LEU* 3.4 37.0 - - + +
266C GLY* 1.3 75.5 - - - +
268C ASN* 1.3 79.5 + - - +
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Residues in contact with ASN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLN 5.3 1.3 - - - -
102C THR* 3.6 25.8 + - - +
103C TYR 4.7 0.4 + - - -
104C GLN* 5.1 1.7 + - - +
109C PHE* 2.9 53.1 + - + +
110C ARG* 3.7 7.8 - - - +
111C LEU* 3.3 28.5 - - + -
254C ILE* 3.6 3.6 - - - +
255C ILE 2.8 31.5 + - - +
267C ARG* 1.3 86.6 + - - +
269C SER* 1.3 64.2 + - - +
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Residues in contact with SER 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLN* 3.9 20.1 + - - +
102C THR* 5.5 3.2 + - - -
111C LEU* 3.8 7.8 - - - +
131C ASN* 3.4 17.3 + - - +
252C LEU* 4.7 12.1 - - - +
253C THR 3.1 16.6 - - - -
254C ILE* 4.0 15.0 - - - -
268C ASN* 1.3 79.6 + - - +
270C PHE* 1.3 67.1 + - - +
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Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 4.0 7.4 - - + -
113C PHE* 3.7 29.6 - + + -
126C TYR* 4.7 1.3 - - + -
131C ASN* 3.8 24.7 - - - +
133C MET* 4.1 22.0 - - + -
143C VAL* 4.0 22.9 - - + -
234C TYR* 5.5 0.2 - + - -
236C TYR* 3.3 17.9 - - - -
252C LEU* 3.5 6.0 - - - -
253C THR* 2.9 47.1 + - + -
255C ILE* 4.0 16.6 - - + -
269C SER* 1.3 80.2 - - - +
271C GLU* 1.3 65.8 + - - +
272C VAL* 3.3 27.1 - - + -
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Residues in contact with GLU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 4.9 5.6 - - - +
131C ASN* 3.1 10.9 + - - +
132C LYS* 2.8 50.8 + - + +
133C MET 2.8 25.1 + - - -
164C LYS* 2.7 37.6 + - + +
250C PRO* 4.1 12.6 - - + +
251C ILE 3.5 14.8 - - - +
252C LEU* 3.5 12.5 - - + +
270C PHE* 1.3 76.0 - - - +
272C VAL* 1.3 66.3 + - - +
285C GLU* 4.7 0.3 - - - +
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Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LYS* 4.3 4.0 + - - -
133C MET* 3.4 10.3 - - + +
135C CYS* 4.5 7.0 - - - -
236C TYR* 3.7 27.8 - - + +
240C SER* 4.2 2.6 + - - -
250C PRO* 4.7 3.3 - - - +
251C ILE* 3.1 38.4 + - + +
253C THR* 3.2 28.3 - - - +
270C PHE* 3.3 24.5 - - + +
271C GLU* 1.3 84.0 - - - +
273C ARG* 1.3 66.4 + - - +
274C VAL* 4.0 13.9 - - + -
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Residues in contact with ARG 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LYS* 3.3 21.6 - - - +
133C MET 2.9 7.9 + - - -
134C PHE* 3.4 22.0 - - + -
135C CYS* 3.1 23.4 + - - -
240C SER* 3.4 19.5 - - - +
241C SER* 6.3 0.6 - - - -
248C ARG* 5.8 3.0 + - - +
272C VAL* 1.3 73.8 - - - +
274C VAL* 1.3 62.1 + - - +
275C CYS* 3.6 17.6 + - + +
281C ASP* 2.6 28.6 + - - -
285C GLU* 3.1 27.7 + - - -
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C CYS* 3.3 14.1 - - - +
136C GLN 4.1 1.3 - - - +
137C LEU* 3.8 17.9 - - - +
236C TYR* 3.5 35.0 - - + +
238C CYS 3.0 30.3 - - - +
239C ASN* 3.4 13.8 - - - +
240C SER* 2.7 42.5 + - - +
241C SER 4.6 0.3 + - - -
246C MET* 4.7 6.5 - - + -
251C ILE* 5.3 2.7 - - + -
272C VAL* 4.0 9.9 - - + -
273C ARG* 1.3 72.2 - - - +
275C CYS* 1.3 65.2 + - - +
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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