Contacts of the strand formed by residues 299 - 306 (chain C) in PDB entry 4NY0
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 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLN* 4.8 3.0 + - - -
280C ILE* 3.9 22.7 - - + -
295C ASP 3.7 14.1 - - - +
296C PHE* 3.3 10.6 + - - +
297C THR 4.8 0.9 - - - +
298C GLN* 1.3 75.6 - - - +
300C GLN* 1.3 60.6 - - - +
301C THR 4.2 8.5 - - - +
302C ILE* 4.0 22.7 - - + -
318C LEU* 4.5 7.4 - - + -
319C LYS 3.8 5.4 - - - +
320C ILE* 3.8 15.7 - - + -
344C ILE* 4.3 6.5 - - + -
348C CYS* 3.5 27.9 - - - -
352C ASN* 5.6 0.3 + - - -
358C PHE* 3.6 18.3 - - + -
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Residues in contact with GLN 300 (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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78A LYS* 3.9 7.6 + - - -
79A HIS* 6.2 1.6 - - + -
135A ASN* 3.2 29.3 + - - +
136A GLN* 3.6 35.3 - - + +
139A GLU* 4.0 30.3 - - + +
298C GLN 3.9 5.4 - - - +
299C VAL* 1.3 73.5 - - - +
301C THR* 1.3 67.1 + - - +
319C LYS* 2.8 36.6 + - + +
320C ILE 4.7 0.3 - - - +
321C ALA* 3.4 21.4 - - - +
358C PHE* 3.3 20.6 - - - -
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Residues in contact with THR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 4.5 4.7 - - - +
139A GLU* 3.4 31.6 - - + +
299C VAL* 4.2 1.7 - - - +
300C GLN* 1.3 85.0 - - + +
302C ILE* 1.3 65.6 + - - +
303C GLN* 5.2 2.1 + - - +
317C GLN 3.7 1.0 + - - +
318C LEU* 3.3 7.6 - - - +
319C LYS* 2.9 43.2 + - + +
358C PHE* 3.6 6.7 - - - -
360C ILE* 4.0 33.9 - - + +
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Residues in contact with ILE 302 (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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299C VAL* 4.0 7.0 - - + -
301C THR* 1.3 76.8 - - - +
303C GLN* 1.3 63.0 + - - +
316C LEU* 4.0 6.7 - - + -
317C GLN 3.6 3.6 - - - -
318C LEU* 3.8 21.5 - - + -
341C ALA* 4.0 27.6 - - + -
344C ILE* 3.8 12.3 - - + +
345C ASP* 3.6 48.2 - - + +
348C CYS* 4.4 2.5 - - - -
358C PHE* 3.0 13.4 + - + +
359C ILE* 3.2 14.5 - - + +
360C ILE* 2.8 30.9 + - - +
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Residues in contact with GLN 303 (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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301C THR* 5.2 1.9 + - - +
302C ILE* 1.3 77.7 - - - +
304C TYR* 1.3 63.8 + - - +
305C SER* 6.2 0.7 - - - +
316C LEU* 3.2 7.0 - - - +
317C GLN* 2.8 58.1 + - + +
359C ILE* 5.2 0.2 - - - -
360C ILE* 3.5 35.2 - - + +
362C PRO* 5.2 13.4 - - + +
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Residues in contact with TYR 304 (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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102C MET* 4.3 2.4 - - - +
303C GLN* 1.3 78.4 - - - +
305C SER* 1.3 61.5 + - - +
315C MET 3.3 15.0 - - - +
316C LEU* 3.6 10.1 - - + -
334C LEU* 3.9 20.8 - - + +
337C ALA* 4.6 5.4 - - + +
338C GLU* 3.2 48.8 + - + +
341C ALA* 3.6 26.5 - - + -
359C ILE* 4.0 23.3 - - + -
360C ILE 5.3 1.8 + - - -
361C ARG* 3.5 22.4 + - - -
362C PRO* 6.2 0.8 - - - +
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Residues in contact with SER 305 (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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303C GLN* 6.2 1.1 - - - +
304C TYR* 1.3 75.0 - - - +
306C ASN* 1.3 68.6 + - - +
308C GLU* 5.6 2.6 + - - -
314C GLY* 3.7 0.3 - - - -
315C MET* 2.9 36.5 + - - +
334C LEU* 3.5 18.7 - - - +
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Residues in contact with ASN 306 (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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305C SER* 1.3 84.5 + - - +
307C SER* 1.3 66.7 + - - +
308C GLU* 3.2 15.4 + - + +
312C ARG* 4.2 37.8 - - - +
313C LYS 3.8 7.2 - - - +
315C MET* 4.7 2.8 - - - +
334C LEU* 3.9 33.8 - - - +
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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