Contacts of the strand formed by residues 50 - 54 (chain M) in PDB entry 6NMY
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 50 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M TRP* 3.6 25.1 - - + +
49M ASP* 1.3 81.5 - - - +
51M GLU* 1.3 71.0 + - - +
61M PRO* 3.8 1.2 - - - +
62M ALA* 3.0 30.6 + - + +
65M ASN* 3.3 44.1 + - + +
83M VAL* 3.5 27.4 - - + -
84M ARG 3.3 14.8 - - - +
85M VAL* 4.2 17.9 - - + -
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Residues in contact with GLU 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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49M ASP* 5.0 11.6 - - + +
50M ILE* 1.3 81.0 - - - +
52M CYS* 1.3 63.5 + - - +
53M VAL* 4.1 3.0 + - - +
59M SER* 4.0 16.7 + - - -
60M MET 3.4 12.9 + - - +
61M PRO* 4.5 10.9 - - + +
83M VAL* 3.7 0.5 - - - -
84M ARG* 2.9 59.1 + - + +
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Residues in contact with CYS 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M LEU* 4.5 9.2 - - + -
41M TRP* 3.7 26.0 - - - -
50M ILE* 5.1 0.2 - - - -
51M GLU* 1.3 75.7 - - - +
53M VAL* 1.3 60.4 + - - +
54M LYS 4.3 0.2 + - - -
58M TYR 3.9 0.3 - - - +
59M SER* 3.3 2.8 - - - -
60M MET* 2.9 33.6 + - - +
62M ALA* 4.3 2.0 - - - -
68M CYS* 2.0 51.6 - - + -
70M PHE* 4.0 14.3 - - + -
82M THR 3.4 9.2 - - - +
83M VAL* 4.5 3.4 - - + +
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Residues in contact with VAL 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M LEU* 5.6 0.3 - - - +
51M GLU 4.7 2.5 - - - +
52M CYS* 1.3 78.0 - - - +
54M LYS* 1.3 62.1 + - - +
56M ALA* 3.5 31.2 - - + +
57M ASP 4.1 1.6 - - - +
58M TYR 3.0 12.1 - - - +
59M SER* 4.1 9.2 - - - -
70M PHE* 5.3 2.7 - - - -
80M ASN 3.5 4.0 - - - +
81M TYR* 3.5 3.3 - - - +
82M THR* 2.9 47.6 + - + +
84M ARG* 3.4 42.4 - - + +
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Residues in contact with LYS 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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41I ASN* 4.7 11.0 + - - +
43I GLU* 2.7 45.9 + - + +
52M CYS 4.3 0.4 + - - -
53M VAL* 1.3 68.1 - - - +
55M ASP* 1.3 77.4 + - - +
56M ALA 2.9 13.2 + - - -
57M ASP 3.2 9.2 + - - -
58M TYR* 2.7 30.0 + - + +
70M PHE* 4.4 10.7 - - + -
72M ALA* 3.0 18.4 + - - +
73M ILE* 4.3 3.4 - - + +
74M SER 5.2 1.1 - - - +
79M THR* 5.1 10.1 - - - -
80M ASN 3.6 2.2 - - - +
81M TYR* 3.6 38.6 - - + +
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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