Contacts of the strand formed by residues 275 - 279 (chain A) in PDB entry 1GC5
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 LYS 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU 3.2 7.0 + - - +
236A LEU* 3.1 18.9 - - + -
237A ALA 2.8 23.4 + - - -
273A ASN* 3.9 27.9 + - - +
274A VAL* 1.3 70.9 + - - +
276A SER* 1.3 59.0 + - - +
300A THR* 3.7 26.8 + - + +
347A GLU* 5.0 11.0 + - - +
458A PHE* 3.6 12.0 - - + -
462A PHE* 3.8 30.5 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 3.1 18.4 - - - -
239A ILE* 5.2 0.7 - - - -
266A LEU* 4.7 1.9 - - - +
269A LEU* 4.2 14.2 - - - +
270A ASN* 5.3 1.6 + - - -
274A VAL 3.5 5.0 + - - -
275A LYS* 1.3 74.5 - - - +
277A HIS* 1.3 59.4 + - - +
298A LYS 4.1 4.5 + - - -
299A PHE* 3.1 35.7 - - - -
300A THR* 3.1 11.1 + - - -
301A SER 2.9 24.1 + - - +
458A PHE* 3.9 3.8 - - - -
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Residues in contact with HIS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA 2.7 9.6 + - - +
238A ILE* 3.4 9.7 - - + +
239A ILE* 2.9 26.7 + - - +
276A SER* 1.3 73.5 - - - +
278A PHE* 1.3 69.7 + - - +
279A GLU* 3.0 37.0 + - - +
299A PHE* 3.9 3.9 - - - -
301A SER* 2.6 34.5 - - - -
302A VAL 3.3 7.5 + - - -
303A GLY* 3.2 18.3 + - - -
348A ARG* 3.9 9.3 + - - -
350A HIS* 5.0 2.0 - - - +
454A SER* 3.7 18.0 + - - -
458A PHE* 3.7 32.3 - + + +
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Residues in contact with PHE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.6 13.7 - - + -
240A SER* 4.9 2.0 - - - -
242A LEU* 3.8 28.3 - - + -
243A GLN 6.0 0.4 - - - -
277A HIS* 1.3 76.4 - - - +
279A GLU* 1.3 73.8 + - - +
280A PHE* 3.3 50.7 + + + -
281A ALA 5.5 0.2 - - - -
292A LEU* 4.1 30.1 - - + -
295A LEU* 6.5 0.2 - - + -
296A LEU* 3.8 15.7 - - + -
299A PHE* 3.6 41.3 - + + -
301A SER 2.9 10.9 + - - +
302A VAL* 3.4 3.8 - - + +
303A GLY 3.1 24.4 + - - -
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Residues in contact with GLU 279 (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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121A GLN* 4.1 9.2 - - - +
125A MET* 4.3 13.0 - - + +
238A ILE* 4.3 13.0 - - + -
239A ILE 3.1 18.2 + - - +
240A SER* 4.0 12.8 - - - -
243A GLN* 4.9 2.6 - - - +
277A HIS* 3.0 27.5 - - - +
278A PHE* 1.3 79.0 - - - +
280A PHE* 1.3 60.8 + - - +
281A ALA* 2.8 13.1 + - - +
303A GLY* 4.0 7.2 - - - +
352A HIS* 5.7 1.2 - - - -
450A GLY 4.0 2.1 - - - +
451A ASP* 3.9 22.4 - - - +
454A SER* 3.1 30.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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