Contacts of the strand formed by residues 51 - 58 (chain 0) 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 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450 SER* 3.8 16.6 - - - -
460 GLN 3.7 11.2 - - - +
470 VAL* 4.5 10.8 - - + +
480 VAL* 4.0 0.2 - - - +
500 GLY* 1.3 77.6 + - - -
520 ASN* 1.3 75.0 + - - +
530 TYR* 3.6 31.4 + - + +
690 VAL 3.5 1.0 - - - +
700 PHE* 3.6 2.3 - - - -
710 GLN* 2.8 51.6 + - - +
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Residues in contact with ASN 52 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440 LYS 4.2 0.3 - - - +
450 SER* 3.4 3.1 - - - -
460 GLN* 3.0 64.6 + - - +
480 VAL* 3.8 18.9 - - - +
510 THR* 1.3 72.9 - - - +
530 TYR* 1.3 59.9 + - - +
540 PHE* 3.9 12.3 - - + -
680 ARG* 3.7 30.0 + - + +
690 VAL 3.4 3.3 + - - +
700 PHE* 3.4 31.7 - - - +
830 SER* 4.9 0.4 + - - -
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Residues in contact with TYR 53 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150 GLU* 3.9 14.7 + - - -
160 THR* 6.2 0.7 - - + -
190 ILE* 3.8 31.0 - - + -
430 PHE* 4.2 22.2 - + - -
440 LYS 4.1 1.1 - - - -
450 SER* 4.0 22.4 - - - -
510 THR* 3.6 25.7 + - + +
520 ASN* 1.3 73.0 - - - +
540 PHE* 1.3 61.9 + - - +
550 ILE* 4.0 19.1 + - + +
670 LEU 3.4 1.4 - - - +
680 ARG* 3.2 5.9 - - - +
690 VAL* 2.6 48.8 + - + +
710 GLN* 3.1 41.8 + - + -
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Residues in contact with PHE 54 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430 PHE* 3.0 8.0 - - - +
440 LYS* 2.8 60.9 + - + +
460 GLN* 3.9 18.6 - - + -
520 ASN* 3.9 13.5 - - + -
530 TYR* 1.3 72.4 - - - +
550 ILE* 1.3 61.0 + - - +
670 LEU 3.0 8.1 - - - +
680 ARG* 3.6 28.9 - - + -
950 LEU* 3.4 12.1 - - + +
960 THR 4.1 3.8 - - - -
970 TYR* 3.0 34.8 - + + -
980 PHE* 3.2 57.0 - + - -
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Residues in contact with ILE 55 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160 THR* 3.7 38.6 - - + +
190 ILE* 3.8 30.1 - - + -
200 ALA* 4.2 9.2 - - + +
400 ALA* 3.9 10.3 - - + -
420 SER 3.5 6.1 - - - +
430 PHE* 4.3 1.3 - - + -
530 TYR* 4.2 18.2 - - + +
540 PHE* 1.3 78.8 - - - +
560 LYS* 1.3 62.2 + - - +
570 VAL* 3.7 18.8 - - + +
650 VAL 3.5 1.4 - - - +
660 HIS* 3.4 1.9 - - - -
670 LEU* 2.6 49.5 + - + +
690 VAL* 4.8 3.8 - - + -
950 LEU* 4.0 4.6 - - - +
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Residues in contact with LYS 56 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400 ALA* 3.7 1.0 - - - -
410 VAL* 3.0 37.6 + - + +
420 SER* 2.9 30.0 + - - +
550 ILE* 1.3 71.7 - - - +
570 VAL* 1.3 62.6 + - - +
640 PHE* 3.9 21.6 - - + +
650 VAL 3.7 3.1 - - - -
660 HIS* 3.0 35.5 - - + +
890 LYS* 4.4 0.2 - - - +
900 ALA 2.7 29.7 + - - -
910 LYS* 3.7 15.0 - - - +
930 ASP* 3.0 25.4 + - - +
950 LEU* 3.8 11.8 - - + +
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Residues in contact with VAL 57 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200 ALA* 4.4 4.0 - - + -
380 PHE* 3.6 39.5 - - + -
390 LYS 3.2 22.7 - - - +
400 ALA* 4.2 4.9 - - - +
550 ILE* 3.7 22.9 - - + +
560 LYS* 1.3 81.2 - - - +
580 HIS* 1.3 63.0 + - - +
590 VAL* 3.5 1.7 + - + +
640 PHE* 3.2 7.5 - - - -
650 VAL* 2.9 41.2 + - + +
670 LEU* 3.8 23.3 - - + -
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Residues in contact with HIS 58 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370 VAL* 3.5 14.0 - - + +
380 PHE* 3.5 4.7 + - - -
390 LYS* 2.8 47.1 + - + +
410 VAL* 4.5 6.9 - - + +
560 LYS 4.3 0.4 + - - -
570 VAL* 1.3 70.5 - - - +
590 VAL* 1.3 59.0 + - - +
600 GLY* 3.2 41.6 + - - -
610 ASP 3.6 3.8 + - - -
620 GLU* 3.6 13.0 - - - -
630 ASP 3.3 9.7 + - - -
640 PHE* 3.6 32.8 - + + -
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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