Contacts of the strand formed by residues 62 - 67 (chain X) in PDB entry 4MXV
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 PHE 62 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X GLN* 4.4 10.5 - - - -
47X LEU* 4.0 21.3 - - + -
48X ILE* 4.5 9.0 - - + -
54X ARG* 3.1 28.7 + - - -
58X VAL* 4.0 17.0 - - + -
59X PRO* 3.2 41.0 + - + +
60X SER 3.0 3.3 - - - +
61X ARG* 1.3 94.1 - - + +
63X SER* 1.3 61.6 + - - +
73X LEU* 4.8 5.6 - - + -
74X THR 3.8 2.0 - - - -
75X ILE* 3.6 31.4 - - + -
82X ASP* 3.6 24.7 - - - -
86X TYR* 4.0 15.0 - + - -
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Residues in contact with SER 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X ILE* 3.4 11.6 - - - +
52X SER 5.6 2.0 - - - -
54X ARG* 5.0 4.3 - - - +
60X SER 5.3 1.8 - - - -
61X ARG 4.7 1.3 + - - -
62X PHE* 1.3 76.8 - - - +
64X GLY* 1.3 60.7 + - - +
73X LEU* 3.1 7.4 - - - +
74X THR* 2.9 49.3 + - - -
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Residues in contact with GLY 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X TRP* 4.9 2.0 - - - -
48X ILE* 3.4 11.0 - - - +
51X ALA 3.3 19.5 - - - -
52X SER* 3.1 25.8 + - - +
63X SER* 1.3 78.9 - - - +
65X SER* 1.3 60.9 + - - -
72X THR 3.3 9.6 - - - -
73X LEU* 4.5 1.1 - - - -
74X THR* 5.7 0.2 - - - -
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Residues in contact with SER 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X TRP* 5.3 0.5 + - - -
51X ALA* 4.2 6.6 - - - +
52X SER* 4.8 4.0 - - - -
64X GLY* 1.3 74.7 - - - -
66X GLY* 1.3 67.2 + - - +
71X PHE* 3.6 9.2 - - - +
72X THR* 3.0 40.9 + - - +
74X THR* 5.8 0.4 + - - -
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Residues in contact with GLY 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X SER* 4.5 2.1 + - - -
51X ALA* 3.8 10.9 - - - +
65X SER* 1.3 85.7 + - - +
67X SER* 1.3 64.1 + - - -
70X ASP 3.2 17.5 - - - -
71X PHE* 3.4 16.1 - - - -
72X THR 4.8 0.2 - - - -
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Residues in contact with SER 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X SER 4.6 1.6 - - - -
31X SER* 4.4 12.1 - - - -
66X GLY* 1.3 76.6 - - - -
68X GLY* 1.3 62.1 + - - +
69X THR 3.0 8.6 + - - -
70X ASP* 3.7 9.0 + - - +
71X PHE* 3.7 7.8 - - - -
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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