Contacts of the strand formed by residues 2 - 10 (chain D) in PDB entry 3F7F
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 ALA 2 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 1.3 77.9 - - + +
3D CYS* 1.3 59.7 + - - +
4D LEU 3.6 0.7 - - - -
380D GLU* 3.2 8.1 - - + -
381D SER* 3.8 24.7 - - - +
382D VAL* 4.0 15.0 - - + +
487D ASN* 3.6 5.4 + - - -
492D ASN* 3.3 7.3 - - - +
495D TYR* 4.8 3.5 - - + +
496D ASN* 3.2 30.7 + - - +
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Residues in contact with CYS 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET 4.7 8.5 - - - -
2D ALA* 1.3 76.1 - - - +
4D LEU* 1.3 73.9 + - + +
342D LEU* 4.6 5.2 - - + -
343D ASN* 3.0 35.2 - - - +
379D ILE* 3.8 24.5 - - + -
380D GLU 2.9 6.5 + - - -
486D LEU* 3.8 6.2 - - + +
487D ASN* 2.9 31.2 + - - +
492D ASN* 3.8 8.7 - - - +
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D CYS* 1.3 96.4 + - + +
5D SER* 1.3 63.8 + - - +
340D LEU* 5.0 2.7 - - + -
342D LEU* 4.5 6.3 - - + -
363D LEU* 4.3 5.6 - - + -
365D ILE* 3.9 20.6 - - + -
379D ILE* 4.2 11.0 - - + +
380D GLU 4.4 3.1 - - - +
381D SER* 3.5 16.2 - - - -
382D VAL* 3.0 28.9 + - - +
471D ILE* 3.8 29.6 - - + -
484D TYR* 4.1 22.4 - - + +
485D LYS 3.3 5.8 - - - +
486D LEU* 4.2 14.1 - - + +
487D ASN* 3.5 4.4 + - - -
695D TYR* 4.4 3.8 - - + +
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Residues in contact with SER 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 1.3 74.1 - - - +
6D ARG* 1.3 60.7 + - - +
7D ILE* 4.5 1.1 - - - +
382D VAL* 4.4 5.8 - - - -
483D LEU 3.6 0.2 - - - +
484D TYR* 3.2 10.0 - - - -
485D LYS* 2.7 43.2 + - - +
487D ASN* 2.6 21.6 + - - -
495D TYR* 3.7 18.8 - - - -
621D GLN* 3.2 33.3 + - - -
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Residues in contact with ARG 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D SER* 1.3 75.8 - - - +
7D ILE* 1.3 71.7 + - - +
8D ASP* 2.8 27.5 + - - +
361D SER* 4.2 12.5 + - - +
382D VAL* 3.8 16.5 + - - +
383D ASN 2.8 35.7 + - - -
384D LYS* 4.0 20.2 + - - +
385D SER* 3.5 23.1 - - - +
386D LEU 4.4 0.7 + - - -
388D ASP* 5.4 1.8 + - - -
454D LYS* 4.9 1.4 - - - +
458D ASN* 3.0 44.5 + - - +
482D SER* 3.5 11.6 + - - -
483D LEU 3.7 2.7 - - - +
484D TYR* 3.5 28.0 - - + -
495D TYR* 5.3 1.1 + - - -
621D GLN* 4.3 4.5 - - - +
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Residues in contact with ILE 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D SER* 4.5 2.9 - - - +
6D ARG* 1.3 82.3 - - - +
8D ASP* 1.3 63.2 + - - +
9D ALA 3.6 0.9 + - - -
385D SER* 5.1 0.2 - - - -
483D LEU* 2.8 49.1 + - + +
485D LYS* 4.0 21.5 - - + -
614D ILE* 4.0 19.0 - - + +
617D GLU* 3.5 31.2 - - + +
618D SER* 4.0 26.5 - - - +
621D GLN* 3.9 30.1 - - + +
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Residues in contact with ASP 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 2.8 25.5 + - - +
7D ILE* 1.3 73.0 - - - +
9D ALA* 1.3 59.6 + - - +
10D ASN 4.2 0.9 + - - -
13D GLN* 5.4 1.2 - - - +
385D SER* 3.5 21.9 - - - +
388D ASP* 3.6 2.6 - - - +
454D LYS* 3.1 29.3 + - - +
458D ASN* 3.8 11.4 - - - +
481D HIS 3.9 1.6 - - - +
482D SER* 2.5 29.4 + - - +
613D ILE* 4.7 0.9 - - - +
617D GLU* 3.7 25.5 + - - +
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Residues in contact with ALA 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE 3.6 1.0 + - - +
8D ASP* 1.3 73.4 - - - +
10D ASN* 1.3 60.7 + - - +
11D LEU* 3.7 3.4 + - + -
479D TYR 3.6 1.2 - - - +
480D ASN* 3.3 3.4 - - - -
481D HIS* 2.7 48.3 + - + +
482D SER* 5.4 0.4 - - - -
610D PHE* 4.3 15.3 - - + -
613D ILE* 4.5 14.6 - - + -
614D ILE* 3.6 28.3 - - + -
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Residues in contact with ASN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASP 4.2 2.0 + - - -
9D ALA* 1.3 72.6 - - - +
11D LEU* 1.3 52.1 + - - +
12D LEU* 2.7 32.7 + - - +
13D GLN* 2.8 42.0 + - + +
415D TYR 5.4 6.3 - - - +
416D GLY* 6.1 1.3 - - - -
418D GLN* 3.0 28.0 + - - +
419D ILE* 4.4 14.1 - - + +
479D TYR* 3.1 7.3 + - - +
480D ASN* 2.7 26.6 + - - +
613D ILE* 4.6 8.3 - - - +
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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