Contacts of the strand formed by residues 52 - 57 (chain M) in PDB entry 7K63
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 LEU 52 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23M MET* 3.5 29.8 - - + -
42M CYS* 3.8 7.9 - - - -
48M ILE* 3.7 13.2 - - + -
50M SER 3.0 4.0 + - - -
51M TYR* 1.3 76.9 - - - +
53M SER* 1.3 70.0 + - - +
54M TRP* 3.1 39.5 - - + +
69M TYR* 3.4 4.4 + - - +
70M ALA* 2.8 29.2 + - + -
90M PHE* 3.5 45.5 - - + -
107M CYS* 4.1 2.7 - - + -
108M LEU 3.4 8.7 - - - +
110M HIS* 4.4 0.2 - - - -
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Residues in contact with SER 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M LEU* 1.3 77.8 + - - +
54M TRP* 1.3 64.3 + - - +
55M TYR* 3.9 12.6 - - - -
67M ILE 3.2 14.4 - - - -
68M TYR* 3.8 5.7 - - - -
106M TYR 3.7 0.5 - - - +
107M CYS* 3.2 5.4 - - - -
108M LEU* 2.7 34.6 + - - +
110M HIS* 3.4 10.4 - - - -
255M THR* 2.7 38.2 + - - -
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Residues in contact with TRP 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLN* 3.5 26.2 - - - -
40M ILE* 3.8 26.9 - - + -
41M THR 4.4 0.2 - - - -
42M CYS* 3.6 33.0 - - + -
52M LEU* 3.1 26.5 - - + +
53M SER* 1.3 74.8 - - - +
55M TYR* 1.3 65.0 + - - +
65M THR* 3.8 2.1 + - - -
66M LEU* 2.9 27.7 + - + -
67M ILE* 3.0 32.1 + - + +
70M ALA 5.2 4.6 + - - -
90M PHE* 4.8 1.8 - - - +
91M SER 3.9 16.2 + - - -
92M LEU* 3.6 54.3 - - + -
105M TYR* 4.7 4.7 - - + -
106M TYR 3.4 4.7 - - - -
107M CYS* 3.9 21.5 - - + -
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Residues in contact with TYR 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M SER* 3.9 13.5 - - - -
54M TRP* 1.3 74.9 - - - +
56M GLN* 1.3 60.1 + - - +
57M GLN 4.1 0.2 - - - -
63M PRO* 4.2 12.6 - - + -
64M LYS 3.4 4.5 - - - +
65M THR* 3.7 22.7 - - - -
66M LEU* 4.0 3.1 - - - -
104M THR 4.4 0.2 - - - -
105M TYR* 3.1 11.6 - - - +
106M TYR* 2.8 47.6 + - + +
108M LEU* 3.3 34.1 - - + +
117M PHE* 4.3 9.9 - + + -
194M LEU* 6.1 0.2 - - + -
255M THR* 2.6 25.5 + - - -
256M LEU* 3.0 38.5 + - + +
259M TRP* 3.5 28.3 - + - -
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Residues in contact with GLN 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M TYR* 1.3 73.9 - - - +
57M GLN* 1.3 59.3 + - - +
58M LYS* 3.1 29.3 + - - +
62M SER 4.3 0.9 - - - +
63M PRO* 3.3 1.2 - - - +
64M LYS* 2.7 59.1 + - + +
66M LEU* 3.5 19.9 - - + +
81M PHE* 3.5 22.2 - - - -
100M ASP 4.1 6.2 + - - +
101M ASP* 4.1 6.1 + - - +
103M ALA* 3.5 20.4 - - + -
104M THR 3.6 2.5 - - - -
105M TYR* 3.1 27.5 + - + -
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Residues in contact with GLN 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M GLN* 1.3 72.7 - - - +
58M LYS* 1.3 66.5 + - - +
59M PRO* 3.8 2.3 - - + +
60M TRP 5.6 2.0 - - - +
61M LYS 3.3 24.5 + - - +
63M PRO* 3.7 29.3 - - + +
103M ALA* 3.5 3.3 - - - -
104M THR* 2.7 42.3 + - - +
106M TYR* 3.1 23.3 + - + -
188M GLN* 2.6 47.3 + - - +
194M LEU* 4.2 0.5 - - - +
244M TYR* 3.4 7.9 + - - -
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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