Contacts of the strand formed by residues 40 - 46 (chain D) in PDB entry 2K8M
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 PRO 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.8 20.9 - - + -
38D SER* 3.1 19.7 - - - +
39D ASP* 1.3 85.1 - - - +
41D TYR* 1.3 54.2 + - - +
59D HIS* 2.8 39.1 + - - +
62D THR* 3.3 20.2 - - + +
63D LEU* 5.1 0.9 - - + -
65D PRO* 4.6 4.0 - - + +
89D VAL* 3.6 20.9 - - + -
90D TYR 3.1 7.2 - - - +
91D ASP* 3.8 9.0 - - + -
101D ILE* 5.2 3.6 - - + -
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Residues in contact with TYR 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 ASP 4.2 7.6 - - - -
40D PRO* 1.3 74.6 - - - +
42D VAL* 1.3 67.8 + - - +
43D LYS* 3.3 25.0 + - + -
55D GLU* 2.7 46.8 + - + -
56D THR* 3.6 13.0 - - - +
57D LYS 3.4 25.4 - - - +
58D VAL* 4.1 19.7 - - + -
59D HIS* 3.7 5.8 - - - -
89D VAL* 3.3 3.1 - - - -
90D TYR* 2.7 68.1 + + + +
92D PHE* 4.6 12.3 - + + +
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Residues in contact with VAL 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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6D LEU* 4.7 16.4 - - + -
23D ILE* 4.4 17.9 - - + -
41D TYR* 1.3 75.9 - - - +
43D LYS* 1.3 59.7 + - - +
44D VAL* 4.1 1.3 + - - +
54D PHE 4.3 0.3 - - - +
56D THR* 2.6 54.1 + - + +
59D HIS* 4.7 6.0 - - + -
69D GLU* 5.4 1.8 - - - +
87D MET* 3.4 33.2 - - + +
88D ALA 3.4 2.9 - - - +
89D VAL* 4.0 20.2 - - + -
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Residues in contact with LYS 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 TYR* 3.3 23.6 + - + -
42D VAL* 1.3 74.8 - - - +
44D VAL* 1.3 65.8 + - - +
45D PHE* 3.4 37.2 + - + -
53D LYS* 6.6 0.2 - - + -
54D PHE 3.8 6.7 - - - +
55D GLU* 2.7 45.4 + - - +
87D MET* 4.3 1.6 - - - -
88D ALA 2.8 38.8 + - - +
90D TYR* 3.7 25.5 - - + -
100D ILE* 5.0 6.1 - - + -
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D VAL 4.1 0.8 - - - +
43D LYS* 1.3 73.0 - - - +
45D PHE* 1.3 69.1 + - - +
46D LEU* 5.1 3.4 - - + -
52D LYS 4.7 0.6 - - - +
53D LYS* 3.8 16.6 - - - +
54D PHE* 3.3 32.3 + - + +
56D THR* 6.4 1.8 - - + -
71D PHE* 3.5 54.1 - - + -
85D LEU* 5.9 4.5 - - + -
86D VAL 3.9 6.3 - - - +
87D MET* 3.6 30.3 - - + -
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Residues in contact with PHE 45 (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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43D LYS* 3.4 48.4 + - + -
44D VAL* 1.3 80.4 - - - +
46D LEU* 1.3 71.9 + - - +
50D LYS* 5.1 12.6 - - - -
52D LYS 5.5 1.3 - - - -
53D LYS* 4.3 22.4 - - + -
86D VAL* 2.9 49.2 + - + +
88D ALA* 4.3 11.4 - - + -
100D ILE* 4.5 13.5 - - + -
128D LYS* 5.9 1.8 - - - -
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Residues in contact with LEU 46 (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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44D VAL* 5.1 2.2 - - + -
45D PHE* 1.3 92.6 - - - +
47D LEU* 1.3 82.5 + - + +
49D ASP* 4.4 2.7 - - - +
50D LYS* 3.6 29.0 - - - +
52D LYS* 3.6 40.6 + - + +
71D PHE* 4.9 7.2 - - + -
73D PHE* 3.8 24.9 - - + -
83D LYS* 4.2 3.8 - - + -
84D THR 3.3 22.7 - - - +
85D LEU* 3.7 13.2 - - + -
86D VAL* 4.9 3.9 - - - +
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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