Contacts of the strand formed by residues 39 - 47 (chain 1) 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 LYS 39 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171 GLN* 3.5 7.9 - - - +
371 VAL* 5.3 3.8 - - + -
381 PHE* 1.3 73.1 - - - +
401 ALA* 1.3 74.7 + - - +
411 VAL* 3.4 17.2 + - + +
571 VAL* 3.8 2.9 - - - -
581 HIS* 2.8 57.9 + - + +
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Residues in contact with ALA 40 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 ALA* 3.3 13.6 - - + +
161 THR* 3.8 29.4 - - + +
171 GLN* 2.7 32.9 + - - +
201 ALA* 4.3 4.9 - - + +
381 PHE 3.8 1.0 + - - -
391 LYS* 1.3 81.9 - - - +
411 VAL* 1.3 59.1 + - - +
551 ILE* 3.9 9.9 - - + -
561 LYS 3.7 5.6 - - - -
571 VAL* 4.2 6.3 - - - +
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Residues in contact with VAL 41 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111 PRO* 3.5 6.9 - - - +
121 ALA* 3.0 17.4 + - - -
391 LYS* 3.6 28.0 - - - +
401 ALA* 1.3 75.1 - - - +
421 SER* 1.3 63.7 + - - +
561 LYS* 2.8 50.2 + - + +
581 HIS* 4.3 13.9 - - + -
641 PHE* 4.3 11.9 - - + -
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Residues in contact with SER 42 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91 THR* 3.6 18.1 - - - +
101 GLN 3.1 17.0 - - - -
111 PRO* 4.1 1.1 - - - -
121 ALA* 3.6 4.2 - - - +
161 THR* 4.8 1.1 - - - -
401 ALA 3.9 0.2 - - - -
411 VAL* 1.3 87.1 - - - +
431 PHE* 1.3 65.9 + - - +
551 ILE* 3.5 5.6 - - - +
561 LYS* 2.9 44.5 + - - +
951 LEU* 4.1 1.6 - - - +
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Residues in contact with PHE 43 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81 ALA 4.1 0.5 - - - +
91 THR* 3.4 3.0 - - - +
101 GLN* 2.8 73.5 + - + +
111 PRO 3.5 19.7 - - - -
121 ALA* 4.1 0.7 - - - -
131 THR* 4.6 9.4 - - + -
161 THR* 3.4 37.7 - - + -
421 SER* 1.3 78.5 - - - +
441 LYS* 1.3 71.9 + - - +
451 SER* 4.2 15.9 - - - -
531 TYR* 4.4 15.5 - + - -
541 PHE 3.1 13.9 - - - +
551 ILE* 4.2 4.7 - - + -
951 LEU* 3.6 6.3 - - - -
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Residues in contact with LYS 44 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 ALA* 4.1 17.7 - - - +
91 THR* 3.7 12.5 + - - +
101 GLN* 5.4 0.4 - - - +
431 PHE* 1.3 80.8 - - - +
451 SER* 1.3 63.8 + - - +
521 ASN 3.9 0.5 - - - +
531 TYR* 3.6 1.7 - - - -
541 PHE* 2.8 48.1 + - + +
941 GLU* 4.9 3.6 + - - -
951 LEU* 3.0 31.6 + - + +
961 THR* 4.7 2.0 - - - +
971 TYR* 3.8 45.4 - - + +
1011 SO4 2.8 32.0 + - - +
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Residues in contact with SER 45 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101 GLN* 5.2 5.4 + - - +
431 PHE* 3.9 11.7 - - - -
441 LYS* 1.3 76.4 - - - +
461 GLN* 1.3 61.9 + - - +
471 VAL* 5.8 1.5 - - - +
511 THR* 4.0 7.2 - - - -
521 ASN 3.4 3.8 - - - -
531 TYR* 3.5 31.9 - - - -
971 TYR* 4.5 6.2 + - - -
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Residues in contact with GLN 46 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 SER* 1.3 77.6 - - - +
471 VAL* 1.3 72.5 + - - +
481 VAL* 3.4 9.4 + - + +
511 THR* 3.5 3.1 - - - +
521 ASN* 2.8 64.6 + - + +
541 PHE* 3.9 11.8 - - + -
681 ARG* 5.2 2.8 - - - +
971 TYR* 3.6 40.4 - - + +
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Residues in contact with VAL 47 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 SER 5.8 0.7 - - - +
461 GLN* 1.3 77.2 - - - +
481 VAL* 1.3 76.4 + - - +
501 GLY 3.8 7.6 - - - +
511 THR* 4.7 9.4 - - + +
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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