Contacts of the strand formed by residues 46 - 55 (chain M) in PDB entry 4UJ3
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 VAL 46 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43M THR* 6.1 0.2 - - - -
44M ILE 3.8 1.0 + - - -
45M GLY* 1.3 79.5 - - - +
47M GLU* 1.3 72.2 + - - +
65M TRP* 3.4 22.2 - - + -
66M ASP 3.9 10.8 - - - +
67M THR* 4.0 11.0 - - - +
76M ILE* 4.5 12.8 - - + +
80M TYR* 4.2 13.0 - - + -
742O ILE* 3.1 21.0 - - + +
746O MET* 3.3 35.0 - - + -
753O LEU* 3.6 23.2 - - + +
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Residues in contact with GLU 47 (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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28M LEU* 4.7 9.5 - - + +
43M THR* 4.5 18.8 - - + +
44M ILE 4.9 8.0 - - - +
46M VAL* 1.3 86.1 - - - +
48M PHE* 1.3 66.8 + - - +
65M TRP* 3.3 4.2 - - - +
66M ASP* 2.9 36.5 + - + +
753O LEU* 3.3 9.0 - - - +
755O VAL* 3.4 29.7 - - + +
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Residues in contact with PHE 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M LEU* 5.0 2.7 - - - -
47M GLU* 1.3 78.0 - - - +
49M ALA* 1.3 60.3 + - - +
50M THR* 3.9 13.7 - - + -
63M GLN* 3.5 34.5 - - + -
64M ILE 2.9 23.3 - - - +
65M TRP* 3.6 36.1 - + + -
750O PRO 3.6 18.4 - - - -
751O SER* 4.4 8.3 - - - -
753O LEU* 3.2 11.0 + - + -
754O GLU* 3.3 46.2 - - + +
755O VAL* 2.8 27.8 + - - -
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Residues in contact with ALA 49 (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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28M LEU* 3.7 13.1 - - + +
32M THR* 3.6 31.2 - - + +
48M PHE* 1.3 75.0 - - - +
50M THR* 1.3 65.5 + - - +
62M ALA 3.8 0.2 - - - +
63M GLN* 4.0 0.2 - - - -
64M ILE* 2.9 34.5 + - - +
754O GLU* 4.9 0.4 - - - -
755O VAL* 4.5 7.4 - - + -
756O LYS* 4.1 20.0 - - + +
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Residues in contact with THR 50 (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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32M THR* 4.1 12.5 - - - +
48M PHE* 3.9 22.2 - - + -
49M ALA* 1.3 79.7 - - - +
51M ARG* 1.3 64.7 + - - +
61M LYS* 4.1 32.0 + - + -
62M ALA 3.2 13.9 - - - +
63M GLN* 4.0 11.7 - - + +
754O GLU* 3.1 18.7 + - - +
756O LYS* 4.1 11.1 - - - +
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Residues in contact with ARG 51 (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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30M ARG 5.3 0.6 + - - -
31M PHE* 3.0 63.0 + - + +
32M THR* 4.5 9.1 - - + +
50M THR* 1.3 77.7 - - - +
52M SER* 1.3 73.5 + - - +
53M ILE* 4.2 7.5 + - - +
60M ILE 3.7 0.3 - - - +
61M LYS* 4.5 1.3 - - - -
62M ALA* 2.7 42.6 + - - +
162M GLU* 2.8 41.8 + - - -
166M GLN* 5.8 0.8 - - - +
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Residues in contact with SER 52 (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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8M TYR* 5.2 2.7 - - - +
51M ARG* 1.3 81.8 + - - +
53M ILE* 1.3 69.6 + - - +
54M GLN* 6.0 1.6 - - - -
59M THR* 5.6 5.8 - - - -
60M ILE 3.0 11.0 - - - -
61M LYS* 3.6 27.9 + - - +
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Residues in contact with ILE 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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31M PHE* 4.3 17.7 - - + -
51M ARG* 4.3 19.3 - - + +
52M SER* 1.3 80.9 - - - +
54M GLN* 1.3 64.6 + - - +
55M VAL* 3.5 24.9 - - + -
59M THR* 3.4 2.1 - - - -
60M ILE* 2.5 55.2 + - + +
166M GLN* 3.9 35.7 - - - +
169M LEU* 3.3 35.9 - - + -
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Residues in contact with GLN 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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52M SER* 6.0 1.8 - - - -
53M ILE* 1.3 76.4 + - - +
55M VAL* 1.3 65.1 + - - +
57M GLY* 3.5 16.3 - - - +
58M LYS 3.5 6.6 - - - +
59M THR* 3.0 41.6 - - - +
166M GLN* 4.1 12.5 + - - +
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Residues in contact with VAL 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 ILE* 3.5 26.9 + - + -
54M GLN* 1.3 78.8 - - - +
56M ASP* 1.3 73.7 + - + +
57M GLY 4.4 0.2 - - - +
58M LYS* 2.9 20.8 + - - +
60M ILE* 4.1 14.8 - - + +
166M GLN* 4.4 2.2 - - - +
169M LEU* 4.9 1.3 - - + -
170M THR* 3.3 47.3 - - + +
173M TYR* 3.3 31.4 - - + -
174M ARG* 5.6 2.9 - - - +
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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