Contacts of the strand formed by residues 51 - 60 (chain 4) in PDB entry 4N6V
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 THR 51 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454 SER* 3.8 13.2 - - - -
464 GLN 3.4 14.6 - - - +
474 VAL* 4.5 10.9 - - + +
484 VAL* 3.9 2.1 - - - +
504 GLY* 1.3 77.7 + - - -
524 ASN* 1.3 71.5 + - - +
534 TYR* 3.6 35.9 + - + +
694 VAL 3.5 1.7 - - - +
704 PHE* 3.6 1.3 - - - -
714 GLN* 2.7 50.4 + - - +
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Residues in contact with ASN 52 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454 SER* 3.2 5.7 - - - -
464 GLN* 2.8 57.4 + - - +
484 VAL* 3.7 17.5 - - - +
514 THR* 1.3 73.2 - - - +
534 TYR* 1.3 59.8 + - - +
544 PHE* 3.8 22.1 - - + -
684 ARG* 3.5 29.0 + - + +
694 VAL 3.3 4.0 + - - +
704 PHE* 3.3 35.8 - - - +
834 SER* 4.9 0.4 + - - -
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Residues in contact with TYR 53 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 GLU* 4.0 15.5 + - - -
164 THR* 6.2 0.4 - - + -
194 ILE* 3.7 32.9 - - + +
434 PHE* 4.2 23.8 - + - -
444 LYS 3.6 1.3 - - - -
454 SER* 4.1 15.9 - - - -
514 THR* 3.6 31.5 + - + +
524 ASN* 1.3 72.3 - - - +
544 PHE* 1.3 62.0 + - - +
554 ILE* 4.0 19.5 + - + -
674 LEU 3.4 1.2 - - - +
684 ARG* 3.4 4.2 - - - +
694 VAL* 2.8 41.2 + - + +
714 GLN* 3.3 40.2 + - + -
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Residues in contact with PHE 54 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434 PHE* 3.0 6.4 - - - +
444 LYS* 2.8 51.2 + - + +
464 GLN* 3.6 26.5 - - - -
524 ASN* 3.8 16.4 - - + -
534 TYR* 1.3 72.6 - - - +
554 ILE* 1.3 60.3 + - - +
674 LEU 3.2 4.7 - - - +
684 ARG* 3.5 28.9 - - + -
954 LEU* 3.3 14.3 - - + +
964 THR 4.2 1.3 - - - +
974 TYR* 3.3 38.4 - + + -
984 PHE* 3.3 55.2 - + - -
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Residues in contact with ILE 55 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164 THR* 3.8 14.6 - - + +
194 ILE* 3.7 35.2 - - + -
204 ALA* 4.2 9.0 - - + +
404 ALA* 3.8 16.2 - - + -
424 SER 3.4 10.8 - - - +
434 PHE* 4.1 8.1 - - + -
534 TYR* 4.1 16.6 - - + +
544 PHE* 1.3 79.9 - - - +
564 LYS* 1.3 64.8 + - - +
574 VAL* 3.6 23.5 + - + +
654 VAL 3.6 1.2 - - - +
664 HIS* 3.2 3.8 - - - -
674 LEU* 2.8 39.4 + - + +
694 VAL* 4.5 9.2 - - + -
954 LEU* 4.0 5.3 - - - +
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Residues in contact with LYS 56 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404 ALA* 3.5 3.3 - - - -
414 VAL* 2.8 42.2 + - + +
424 SER* 2.9 29.2 + - - +
554 ILE* 1.3 71.1 - - - +
574 VAL* 1.3 61.0 + - - +
644 PHE* 3.9 20.2 - - + +
654 VAL 3.7 2.9 - - - -
664 HIS* 2.9 34.8 - - + +
904 ALA 2.8 25.5 + - - -
914 LYS* 3.6 16.2 - - - +
934 ASP* 2.8 27.5 + - - +
954 LEU* 3.9 12.7 - - + +
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Residues in contact with VAL 57 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204 ALA* 4.4 4.9 - - + -
384 PHE* 3.6 32.1 - - + -
394 LYS 3.4 26.2 - - - +
404 ALA* 4.0 4.3 - - - +
554 ILE* 3.6 23.3 - - + +
564 LYS* 1.3 79.5 - - - +
584 HIS* 1.3 67.0 + - - +
594 VAL* 3.5 3.3 + - + +
644 PHE* 3.2 8.9 - - - -
654 VAL* 2.8 37.7 + - + +
674 LEU* 3.8 26.2 - - + -
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Residues in contact with HIS 58 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374 VAL* 3.6 20.9 - - + +
384 PHE* 3.3 8.7 + - - -
394 LYS* 2.8 67.8 + - + +
414 VAL* 4.5 0.6 - - + +
574 VAL* 1.3 71.3 - - - +
594 VAL* 1.3 59.6 + - - +
604 GLY* 3.4 19.7 - - - -
614 ASP* 3.5 2.5 + - - -
624 GLU* 3.1 34.5 - - + -
634 ASP 3.3 9.7 + - - -
644 PHE* 3.4 29.2 - + + -
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Residues in contact with VAL 59 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354 PHE* 3.7 38.2 - - + -
364 PRO* 5.9 1.0 - - - +
374 VAL* 3.3 18.0 + - - +
384 PHE* 3.9 17.9 - - + -
574 VAL* 3.9 9.2 - - + +
584 HIS* 1.3 78.6 - - - +
604 GLY* 1.3 58.0 + - - +
634 ASP* 2.9 37.5 + - + +
644 PHE 4.0 3.1 - - - +
654 VAL* 4.0 23.1 - - + -
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Residues in contact with GLY 60 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374 VAL* 3.5 18.3 - - - +
584 HIS* 3.4 14.3 - - - -
594 VAL* 1.3 79.1 - - - +
614 ASP* 1.3 73.5 + - - +
624 GLU 3.3 2.5 - - - -
634 ASP* 2.9 23.2 + - - +
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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