Contacts of the strand formed by residues 36 - 43 (chain D) in PDB entry 3RIK
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D PRO* 3.1 22.1 - - - +
33D ALA* 2.8 34.2 + - + +
34D LEU 4.5 2.5 - - - +
35D GLY* 1.3 81.2 + - - +
37D PHE* 1.3 59.4 + - - +
53D MET* 3.9 23.9 - - + +
54D GLY 3.4 13.5 - - - +
55D PRO* 5.2 2.2 - - + -
56D ILE* 3.5 13.0 - - - +
494D TRP* 3.6 9.2 - - - +
495D HIS 4.8 1.6 + - - +
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Residues in contact with PHE 37 (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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32D PRO* 4.2 4.7 - - - -
36D THR* 1.3 74.1 - - - +
38D SER* 1.3 71.9 + - - +
39D ARG* 3.8 39.3 - - + -
53D MET* 3.1 7.4 - - - +
54D GLY* 2.9 64.7 + - - -
55D PRO* 3.2 28.3 - - + -
56D ILE* 4.0 4.7 - - + -
480D LEU* 3.5 39.9 - - + -
481D GLU 4.4 11.4 - - - -
492D TYR* 3.9 10.5 - + - -
493D LEU 3.3 13.0 - - - +
494D TRP* 4.1 7.0 - - + -
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Residues in contact with SER 38 (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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30D THR 4.8 3.6 + - - -
32D PRO* 3.2 28.2 - - - +
37D PHE* 1.3 77.5 - - - +
39D ARG* 1.3 60.5 + - - +
40D TYR* 4.6 1.6 - - - -
51D LEU* 4.3 15.1 - - - +
52D SER 3.4 7.2 - - - -
53D MET* 4.4 4.1 - - - +
491D THR 4.4 0.2 - - - -
492D TYR* 3.2 5.7 - - - -
493D LEU* 2.8 52.5 + - - +
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Residues in contact with ARG 39 (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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37D PHE* 3.8 25.4 - - + -
38D SER* 1.3 74.8 - - - +
40D TYR* 1.3 72.1 + - - +
41D GLU* 4.2 14.8 - - - -
50D GLU 3.2 2.4 - - - +
51D LEU* 3.5 3.5 - - - +
52D SER* 2.7 64.9 + - - +
53D MET 4.9 3.6 + - - +
481D GLU 4.6 1.2 + - - -
482D THR* 2.9 28.5 + - - +
490D HIS* 4.0 19.7 + - + +
491D THR 3.4 4.3 - - - +
492D TYR* 3.5 30.0 + - + -
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Residues in contact with TYR 40 (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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26D PHE* 4.2 21.5 - + - -
29D PRO* 6.0 1.7 - - - +
30D THR 5.3 5.9 + - - -
38D SER* 4.6 2.5 - - - -
39D ARG* 1.3 76.6 - - - +
41D GLU* 1.3 60.3 + - - +
49D MET* 3.6 22.2 - - + -
50D GLU 3.2 6.3 - - - -
51D LEU* 3.5 39.8 - - + +
422D HIS* 3.3 11.9 - - + -
425D LYS* 4.9 3.9 - - - -
426D PHE* 3.3 49.6 - + + -
490D HIS* 3.1 7.8 - - - +
491D THR* 2.8 36.9 + - - +
493D LEU* 3.7 20.9 - - + -
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Residues in contact with GLU 41 (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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39D ARG* 4.2 13.2 - - - -
40D TYR* 1.3 73.9 - - - +
42D SER* 1.3 62.9 + - - +
43D THR* 4.1 12.7 - - + +
47D ARG* 3.1 37.7 + - - +
48D ARG 3.8 1.4 - - - -
49D MET 3.1 3.9 + - - -
50D GLU* 2.9 38.3 + - + +
52D SER* 5.8 0.4 - - - +
422D HIS* 4.1 0.4 - - - -
485D PRO* 3.6 17.5 - - - +
489D ILE 3.6 2.9 - - - -
490D HIS* 2.9 34.8 + - + +
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Residues in contact with SER 42 (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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41D GLU* 1.3 70.5 - - - +
43D THR* 1.3 63.6 + - - +
47D ARG 3.1 9.2 - - - -
48D ARG* 3.6 2.1 - - - -
49D MET* 2.7 29.1 + - - +
357D TRP* 3.6 12.6 - - - -
418D TYR* 4.1 9.0 - - - +
422D HIS* 2.9 23.3 + - - -
488D SER* 3.2 6.4 - - - -
489D ILE* 2.9 41.5 + - - -
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Residues in contact with THR 43 (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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41D GLU* 4.1 20.6 - - + +
42D SER* 1.3 79.9 - - - +
44D ARG* 1.3 66.4 + - - +
45D SER* 2.9 23.3 + - - +
46D GLY 2.8 12.3 + - - -
47D ARG* 2.7 52.8 + - + +
48D ARG* 2.8 17.2 + - - -
357D TRP* 3.4 6.3 - - - -
485D PRO* 5.0 7.0 - - + -
486D GLY 6.0 0.2 - - - +
487D TYR 3.8 5.8 - - - +
488D SER* 4.2 10.1 - - - -
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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