Contacts of the strand formed by residues 57 - 64 (chain M) in PDB entry 5X6E
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 ILE 57 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M LYS* 5.6 1.3 - - - +
49M THR* 5.5 4.9 - - + -
50M SER 3.2 9.9 - - - +
51M ILE* 3.6 28.3 - - + +
55M GLY 3.0 15.6 + - - +
56M THR* 1.3 82.9 - - - +
58M MET* 1.3 67.9 + - - +
59M ASN* 3.9 11.9 - - - +
176M TYR* 3.3 63.1 - - + +
136N ILE* 4.6 4.9 - - - +
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Residues in contact with MET 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M THR* 3.3 2.8 - - - -
50M SER* 2.8 38.0 + - - +
56M THR 5.4 0.2 - - - +
57M ILE* 1.3 80.7 - - - +
59M ASN* 1.3 79.7 + - - +
60M LEU* 3.3 18.1 + - + -
176M TYR* 3.7 7.6 - - - +
177M SER 3.9 5.4 - - - +
178M SER 3.3 22.2 - - - +
179M GLY* 5.0 2.2 - - - -
131N PHE* 4.1 16.8 - - + +
132N ASN* 3.2 27.4 - - - +
135N SER* 3.8 30.1 - - - +
136N ILE* 4.1 15.9 - - + -
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Residues in contact with ASN 59 (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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47M LYS* 3.3 36.5 + - - +
48M LEU 4.0 2.9 - - - -
49M THR* 3.5 20.8 - - - +
57M ILE* 3.9 9.8 - - - +
58M MET* 1.3 78.3 - - - +
60M LEU* 1.3 66.0 + - - +
61M GLN 3.8 1.3 - - - +
62M TYR* 3.8 14.9 + - + -
173M GLU* 3.7 17.2 + - - -
176M TYR* 3.1 33.5 + - - +
177M SER* 3.4 24.9 + - - +
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Residues in contact with LEU 60 (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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48M LEU* 3.0 42.1 + - + +
49M THR 4.6 0.7 - - - +
50M SER* 4.7 3.6 - - - -
58M MET* 3.6 15.9 - - + +
59M ASN* 1.3 74.6 - - - +
61M GLN* 1.3 63.2 + - - +
83M TYR* 3.4 40.8 - - + -
130M LYS* 3.0 18.9 + - - +
128N LEU* 4.1 28.0 - - + +
131N PHE* 3.4 20.4 - - + -
132N ASN* 4.1 28.9 - - + +
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Residues in contact with GLN 61 (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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47M LYS* 3.6 1.6 - - - +
48M LEU* 3.0 32.7 + - + +
59M ASN* 4.7 1.7 - - - +
60M LEU* 1.3 82.3 + - - +
62M TYR* 1.3 85.4 + - - +
63M TYR* 2.9 30.6 + - + -
123M GLN* 2.9 24.4 + - - +
126M TYR* 3.0 35.4 - - + +
127M SER* 4.5 3.0 + - - -
130M LYS* 3.6 12.8 - - - +
177M SER* 5.5 1.1 - - - -
301M GSH 3.6 16.6 - - - +
128N LEU* 3.9 17.0 - - + +
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Residues in contact with TYR 62 (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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45M ILE* 4.3 9.4 - - + -
46M THR 3.4 11.9 - - - +
47M LYS* 4.4 3.8 - - + -
59M ASN* 3.8 15.3 + - + -
61M GLN* 1.3 94.9 - - - +
63M TYR* 1.3 67.7 + - - +
88M ILE* 4.4 14.8 - - + -
146M GLN* 5.1 2.0 - - - -
150M LEU* 5.0 7.4 - - + -
154M TYR* 3.4 23.6 - + - +
166M LEU* 4.3 19.9 - - + +
169M LEU* 4.7 6.0 - - + +
173M GLU* 2.7 41.2 + - - +
174M LEU* 5.6 1.4 - - + +
177M SER* 3.9 22.2 - - - -
301M GSH 2.9 46.2 + - - +
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Residues in contact with TYR 63 (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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41M LEU* 3.6 10.4 - - + +
45M ILE* 3.4 3.3 - - - +
46M THR* 2.6 55.4 + - - +
48M LEU* 4.1 26.4 - - + +
61M GLN* 2.9 22.1 + - - -
62M TYR* 1.3 77.1 - - - +
64M LYS* 1.3 61.4 + - - +
67M PHE* 3.5 40.2 - + + -
68M VAL 4.8 0.2 - - - -
69M ILE* 3.7 34.2 - - + +
85M LEU* 4.2 12.8 - - + -
123M GLN* 2.7 33.6 + - - -
154M TYR* 4.5 0.7 - - - -
301M GSH 3.7 9.9 - - - -
128N LEU* 5.3 0.9 - - - +
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Residues in contact with LYS 64 (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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41M LEU* 4.1 0.8 - - - +
44M GLY 3.6 4.9 - - - +
45M ILE* 3.7 21.3 - - + +
63M TYR* 1.3 75.6 - - - +
65M GLY* 1.3 80.0 + - - +
66M ALA 3.5 2.9 + - - +
67M PHE* 4.5 1.2 - - - +
153M VAL* 3.8 30.8 + - + +
154M TYR* 3.4 40.2 - - + +
301M GSH 3.2 36.3 + - + +
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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