Contacts of the strand formed by residues 299 - 304 (chain A) in PDB entry 1GEY
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 TYR 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ASN* 3.3 34.3 - - - +
156A ASN 2.4 29.5 + - - -
157A ASN* 3.2 10.9 - - - +
158A PRO* 3.0 35.7 - - + -
159A THR 5.1 0.2 - - - -
160A GLY* 3.8 6.1 - - - -
187A TYR* 3.7 25.5 - + - -
295A SER* 2.9 27.0 + - - -
297A THR* 3.1 37.5 + - + +
298A ASN* 1.3 85.6 - - - +
300A ILE* 1.3 66.2 + - - +
335A ARG* 3.9 15.5 - - + -
336A ILE 3.1 12.8 - - - +
337A THR* 4.1 0.4 - - - -
338A VAL* 4.0 1.5 - - - +
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Residues in contact with ILE 300 (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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276A ARG* 3.9 17.7 - - + +
279A LEU* 3.8 34.5 - - + -
280A ILE* 3.4 30.7 - - + +
283A LEU* 4.5 10.3 - - + -
292A VAL* 3.6 28.9 - - + -
293A PHE 4.1 6.1 - - - +
295A SER* 4.6 4.7 - - - +
299A TYR* 1.3 82.0 - - - +
301A LEU* 1.3 67.8 + - - +
302A ALA* 4.8 1.1 - - + +
334A LEU 3.5 2.4 - - - +
335A ARG* 3.4 6.9 - - - -
336A ILE* 2.7 41.0 + - + +
338A VAL* 4.4 2.9 - - + -
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Residues in contact with LEU 301 (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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133A TRP* 4.6 2.0 - - + -
158A PRO* 3.8 24.5 + - + +
159A THR* 3.7 40.5 + - + +
293A PHE* 3.1 48.6 + - + +
295A SER* 5.6 0.2 - - - -
300A ILE* 1.3 77.7 - - - +
302A ALA* 1.3 62.1 + - - +
324A GLN* 4.2 20.6 - - + -
330A LEU* 3.8 17.7 - - + -
333A CYS* 3.7 26.7 - - + -
334A LEU 3.7 9.6 - - - +
335A ARG* 4.5 2.0 - - - -
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Residues in contact with ALA 302 (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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283A LEU* 4.6 11.4 - - + -
289A VAL* 4.7 3.8 - - + -
291A GLN 3.2 12.8 - - - +
292A VAL* 4.3 13.9 - - + -
293A PHE* 4.0 1.6 - - - -
300A ILE* 4.8 2.2 - - + +
301A LEU* 1.3 78.1 - - - +
303A ARG* 1.3 60.3 + - - +
304A PHE* 3.2 27.6 - - + -
333A CYS* 3.1 5.2 - - - -
334A LEU 3.0 31.0 + - - +
336A ILE* 5.3 1.8 - - + -
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Residues in contact with ARG 303 (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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133A TRP* 5.1 5.9 - - - -
289A VAL* 3.8 3.3 - - - +
290A GLU* 2.9 58.5 + - - +
291A GLN* 2.8 28.0 + - + +
293A PHE* 3.8 27.2 - - + -
302A ALA* 1.3 72.0 - - - +
304A PHE* 1.3 64.5 + - - +
329A SER 3.2 25.1 + - - -
331A SER* 3.0 21.8 + - - +
332A GLY* 3.4 11.0 - - - +
333A CYS* 3.8 19.6 - - - -
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Residues in contact with PHE 304 (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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283A LEU* 5.1 1.6 - - + -
288A CYS* 3.5 14.4 - - - +
289A VAL* 3.7 31.6 - - + -
290A GLU* 4.5 7.5 - - - +
302A ALA* 3.2 37.9 - - + -
303A ARG* 1.3 82.2 - - - +
305A LYS* 1.3 63.0 + - - +
306A ALA 3.5 2.6 + - - -
307A SER* 4.0 16.2 + - - -
310A VAL* 4.0 16.2 - - + -
321A LEU* 5.4 1.1 - - + -
332A GLY* 2.8 20.7 + - - +
334A LEU* 3.6 36.1 - - + -
336A ILE* 4.2 18.8 - - + -
351A LEU* 4.0 22.0 - - + -
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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