Contacts of the strand formed by residues 36 - 43 (chain A) in PDB entry 2F61
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 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 3.4 29.9 - - + +
33A ALA* 3.1 22.3 + - - +
34A LEU 4.9 0.7 + - - -
35A GLY* 1.3 80.2 + - - +
37A PHE* 1.3 70.0 + - - +
53A MET* 4.4 2.5 - - + -
54A GLY 3.3 11.7 - - - +
56A ILE* 4.4 3.4 - - - +
494A TRP* 3.8 15.4 - - - +
495A HIS 4.5 2.9 + - - +
140B ASP 5.8 0.2 - - - -
141B ASP* 4.5 5.0 + - - -
142B PHE 6.0 0.4 - - - +
143B GLN* 3.9 23.1 + - + +
145B HIS* 2.9 29.8 - - - -
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Residues in contact with PHE 37 (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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32A PRO* 4.9 0.9 - - - -
36A THR* 1.3 76.6 - - - +
38A SER* 1.3 71.8 + - - +
39A ARG* 3.8 42.0 - - + -
53A MET* 3.3 10.5 - - - +
54A GLY* 2.9 64.1 + - - -
55A PRO* 3.5 15.9 - - + -
56A ILE* 3.9 10.5 - - + -
480A LEU* 3.3 44.4 - - + -
481A GLU 4.9 4.9 - - - -
492A TYR* 3.9 12.3 - + - -
493A LEU 3.3 12.8 - - - +
494A TRP* 3.9 1.8 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR 4.8 0.7 + - - -
32A PRO* 3.4 31.6 - - - +
37A PHE* 1.3 76.2 - - - +
39A ARG* 1.3 60.0 + - - +
40A TYR* 4.3 7.6 - - - -
51A LEU* 4.1 15.0 - - - -
52A SER 3.6 3.6 - - - -
53A MET* 3.4 9.6 - - - +
491A THR 3.6 1.3 - - - +
492A TYR* 3.2 6.9 - - - -
493A LEU* 2.8 45.8 + - - +
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Residues in contact with ARG 39 (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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37A PHE* 3.8 31.4 - - + -
38A SER* 1.3 74.0 - - - +
40A TYR* 1.3 70.9 + - - +
41A GLU* 4.3 11.4 - - - +
50A GLU 3.1 4.5 - - - +
51A LEU* 3.1 2.8 - - - +
52A SER* 2.7 70.6 + - - +
53A MET 5.1 2.6 + - - +
481A GLU 4.6 1.8 + - - -
482A THR* 2.7 31.3 + - - +
490A HIS* 3.6 27.3 - - + +
491A THR 3.6 3.4 - - - +
492A TYR* 3.4 22.1 + - + -
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Residues in contact with TYR 40 (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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26A PHE* 4.3 22.0 - + - -
29A PRO* 5.4 9.5 - - - +
30A THR 5.9 0.2 + - - -
38A SER* 4.4 3.8 - - - -
39A ARG* 1.3 77.9 - - - +
41A GLU* 1.3 59.9 + - - +
49A MET* 3.7 22.9 - - + -
50A GLU 3.0 3.8 - - - -
51A LEU* 3.5 40.6 - - + +
422A HIS* 3.3 12.8 - - + -
425A LYS* 4.7 3.5 - - - -
426A PHE* 3.4 48.3 - + + -
490A HIS* 3.4 3.5 - - - +
491A THR* 3.0 38.6 + - - +
493A LEU* 3.7 18.5 - - + +
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Residues in contact with GLU 41 (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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39A ARG* 4.3 11.4 - - - -
40A TYR* 1.3 74.8 - - - +
42A SER* 1.3 65.8 + - - +
43A THR* 3.8 20.8 - - + +
47A ARG* 3.2 26.6 + - - +
48A ARG 3.5 3.3 + - - -
49A MET 2.8 3.7 + - - -
50A GLU* 2.7 46.5 + - + +
485A PRO* 3.6 19.2 - - - +
489A ILE 3.8 2.7 - - - -
490A HIS* 2.8 34.7 + - + +
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Residues in contact with SER 42 (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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41A GLU* 1.3 71.0 - - - +
43A THR* 1.3 68.0 + - - +
47A ARG 3.1 11.4 - - - -
48A ARG* 3.6 3.0 - - - -
49A MET* 2.6 27.7 + - - +
357A TRP* 3.7 10.5 - - - -
418A TYR* 4.3 8.4 - - - +
419A HIS* 5.7 0.4 - - - -
422A HIS* 2.8 25.6 + - - -
488A SER* 3.4 0.9 - - - -
489A ILE* 3.1 39.3 + - - +
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Residues in contact with THR 43 (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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41A GLU* 3.8 24.0 - - + +
42A SER* 1.3 79.9 - - - +
44A ARG* 1.3 66.2 + - - +
45A SER* 3.0 23.9 + - - +
46A GLY 2.9 12.3 + - - -
47A ARG* 2.9 27.6 + - - +
48A ARG* 3.0 13.9 + - - -
357A TRP* 3.4 7.6 - - - -
485A PRO* 4.9 6.5 - - + -
486A GLY 5.3 0.7 - - - +
487A TYR 3.8 5.2 - - - -
488A SER* 3.7 16.8 - - - -
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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