Contacts of the strand formed by residues 513 - 521 (chain A) in PDB entry 6T2C
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 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A LEU* 5.0 4.3 - - + -
468A SER* 4.4 7.2 - - - +
501A LYS* 4.2 22.2 - - + -
502A GLY 4.4 0.4 - - - +
503A ARG 4.0 19.7 - - - +
504A SER* 4.1 12.8 - - - -
506A LEU* 4.3 9.8 - - + +
511A ASP 3.9 0.2 + - - -
512A VAL* 1.3 72.2 - - - +
514A ASN* 1.3 75.4 + - - +
515A PHE* 4.0 3.5 + - + -
564A GLY* 3.4 0.7 - - - -
565A THR* 2.8 48.8 + - + +
570A MET* 4.1 17.5 - - + -
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Residues in contact with ASN 514 (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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365A LEU* 2.8 36.5 + - + +
366A GLY 4.0 0.8 + - - -
502A GLY* 3.2 27.2 + - - -
503A ARG 4.8 2.4 + - - -
512A VAL* 3.9 10.6 - - - +
513A VAL* 1.3 80.4 - - - +
515A PHE* 1.3 62.7 + - - +
562A THR* 5.0 4.5 - - + -
563A ASN 3.5 11.4 - - - +
564A GLY* 4.4 1.2 - - - -
1V A 3.7 13.6 - - - +
2V G 3.8 21.8 + - - +
10V A 3.5 24.1 + - - +
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Residues in contact with PHE 515 (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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281A LYS* 4.3 22.2 - - + -
365A LEU* 3.7 3.8 - - - -
460A ILE* 6.4 1.1 - - + -
464A LEU* 4.2 18.4 - - + -
499A ILE* 3.7 33.0 - - + -
500A ILE 3.2 15.5 - - - +
501A LYS* 4.2 6.7 - - + -
513A VAL* 4.1 7.9 - - + -
514A ASN* 1.3 76.2 - - - +
516A ILE* 1.3 70.0 + - - +
517A SER* 4.2 13.7 - - - -
562A THR* 3.5 5.2 - - - +
563A ASN* 2.9 58.2 + - + +
564A GLY 3.9 22.0 - - - -
565A THR* 4.0 14.1 - - + -
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Residues in contact with ILE 516 (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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334A TYR* 4.9 3.1 - - + -
337A ILE* 3.7 30.3 - - + -
361A LEU* 4.0 9.6 - - + -
364A GLY* 3.4 36.6 - - - +
365A LEU* 3.7 15.0 - - + -
498A PHE 3.9 0.5 - - - +
499A ILE* 3.3 3.6 - - - -
500A ILE* 2.9 39.7 + - + +
515A PHE* 1.3 78.3 - - - +
517A SER* 1.3 60.9 + - - +
518A LEU* 3.9 13.2 - - + +
560A VAL* 4.0 22.9 - - + -
561A ARG 3.3 10.8 - - - +
562A THR* 4.5 4.9 - - - +
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Residues in contact with SER 517 (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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281A LYS 4.5 13.1 + - - -
498A PHE 3.6 4.7 - - - -
499A ILE* 4.4 10.8 - - - -
515A PHE* 4.1 20.5 + - - -
516A ILE* 1.3 72.9 - - - +
518A LEU* 1.3 60.9 + - - +
519A GLU* 4.1 12.6 - - - +
535A TYR* 5.1 3.6 - - - -
559A TYR 3.1 5.8 + - - +
560A VAL* 3.3 1.0 - - - -
561A ARG* 2.9 47.4 + - - +
563A ASN* 5.4 0.3 - - - +
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Residues in contact with LEU 518 (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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337A ILE* 4.4 15.5 - - + -
338A TRP* 4.4 17.5 - - + -
341A LEU* 3.8 24.7 - - + -
497A GLY* 3.3 2.8 - - - -
498A PHE* 2.9 50.1 + - + +
500A ILE* 4.1 16.2 - - + -
516A ILE* 3.9 12.6 - - + +
517A SER* 1.3 75.0 - - - +
519A GLU* 1.3 61.8 + - - +
558A LEU* 3.8 24.8 - - + +
559A TYR 3.2 5.6 - - - +
560A VAL* 3.7 30.1 - - + -
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Residues in contact with GLU 519 (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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281A LYS 3.7 6.3 - - - +
282A PHE* 3.3 24.1 - - - +
283A LEU* 3.1 47.6 + - + +
287A ALA* 4.5 6.9 - - + +
456A LYS* 5.1 1.2 + - - +
480A ILE* 3.3 27.4 - - + +
496A TYR* 3.8 13.1 - - - +
499A ILE* 5.5 0.5 - - - +
517A SER* 4.5 10.6 - - - +
518A LEU* 1.3 83.4 - - - +
520A PHE* 1.3 65.3 + - - +
521A SER 3.8 0.2 + - - -
535A TYR* 6.5 0.4 - - + -
558A LEU* 3.6 4.3 - - - +
559A TYR* 2.9 34.4 + - - +
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Residues in contact with PHE 520 (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* 4.3 0.2 - - - +
287A ALA* 3.7 5.9 - - - +
288A MET* 3.3 43.1 + - + +
290A LEU* 4.2 26.0 - - + -
311A LEU* 4.3 13.7 - - + -
314A PHE* 6.4 1.6 - + - -
317A TRP* 4.8 5.8 - + - -
338A TRP* 4.6 11.0 - + - -
495A LEU* 4.4 11.2 - - + -
496A TYR* 3.2 33.1 + - - +
497A GLY* 4.1 4.7 - - - -
498A PHE* 4.0 25.1 - + - -
519A GLU* 1.3 78.1 - - - +
521A SER* 1.3 62.3 + - - +
540A ILE* 4.1 19.7 - - + -
556A VAL* 4.7 3.6 - - + -
557A TYR 3.5 6.5 - - - +
558A LEU* 3.7 20.0 - - + -
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Residues in contact with SER 521 (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* 4.2 6.1 - - - -
286A ASP* 2.8 23.1 + - - +
288A MET* 4.1 7.4 - - - +
520A PHE* 1.3 77.8 - - - +
522A LEU* 1.3 73.1 + - - +
523A THR* 3.0 15.8 + - - -
556A VAL* 3.7 7.7 - - - +
557A TYR* 2.9 31.9 + - - -
559A TYR* 3.5 32.1 - - - -
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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