Contacts of the strand formed by residues 85 - 90 (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 THR 85 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36X TYR 3.8 0.5 - - - +
37X GLN* 3.6 1.9 - - - -
38X GLN* 2.8 45.5 + - - +
84X ALA* 1.3 75.8 - - - +
86X TYR* 1.3 65.2 + - - +
87X TYR* 3.7 32.8 + - + +
100X GLN 5.3 0.4 - - - +
101X GLY* 4.0 4.0 - - - -
102X THR 3.2 22.4 - - - +
103X LYS* 3.8 24.2 - - + +
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Residues in contact with TYR 86 (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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6X GLN* 2.4 29.2 + - - +
21X ILE* 4.0 18.2 - - + -
35X TRP* 4.9 3.6 - - + -
36X TYR 3.2 7.2 - - - +
37X GLN* 3.4 32.3 + - + -
47X LEU* 3.8 19.5 - - + -
62X PHE* 4.0 11.2 - + - -
73X LEU* 3.7 24.5 - - + -
75X ILE* 3.7 15.3 - - + +
82X ASP* 2.4 34.6 + - - +
84X ALA* 3.5 21.8 - - + -
85X THR* 1.3 74.0 - - - +
87X TYR* 1.3 55.7 + - - +
101X GLY* 3.4 0.9 - - - -
102X THR 2.8 18.4 + - - -
104X VAL* 3.7 23.1 - - + -
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Residues in contact with TYR 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X GLN* 3.5 1.3 - - - +
35X TRP* 3.2 8.2 - - - -
36X TYR* 2.7 47.7 + - + +
38X GLN* 3.3 31.4 + - + -
44X PRO* 5.6 0.2 - - + -
85X THR* 3.7 25.6 - - + +
86X TYR* 1.3 74.4 - - - +
88X CYS* 1.3 65.6 + - - +
98X PHE* 4.4 12.1 - - + -
99X GLY 3.5 20.2 - - - -
100X GLN 3.7 11.1 + - - -
101X GLY* 3.6 19.3 - - - -
39Y GLN* 3.6 18.5 + - - -
43Y LYS 3.9 8.0 + - - -
44Y GLY* 4.3 11.7 - - - -
45Y LEU* 4.0 17.9 - - + -
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Residues in contact with CYS 88 (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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4X MET* 4.2 4.3 - - - -
6X GLN* 3.3 23.2 + - - -
23X CYS* 2.0 46.0 - - + -
33X VAL* 4.6 2.9 - - + -
34X ALA 3.2 8.5 - - - +
35X TRP* 3.5 24.0 - - + -
87X TYR* 1.3 75.5 - - - +
89X GLN* 1.3 64.6 + - - +
98X PHE* 3.5 5.2 - - - +
99X GLY* 2.9 29.4 + - - -
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Residues in contact with GLN 89 (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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4X MET* 4.1 5.6 - - - -
33X VAL* 3.3 4.0 - - - +
34X ALA* 2.8 38.2 + - - +
36X TYR* 3.4 24.0 + - + -
88X CYS* 1.3 78.9 - - - +
90X GLU* 1.3 71.0 + - - +
91X SER* 3.4 17.2 + - - -
96X TRP* 3.2 30.3 + - - +
97X THR 3.4 6.7 - - - +
98X PHE* 3.2 40.0 - - + +
99X GLY 4.7 0.7 - - - +
99Y PRO 3.9 5.0 - - - +
100Y PHE* 3.3 20.0 - - - -
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Residues in contact with GLU 90 (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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2X ILE* 3.7 25.0 - - + +
4X MET* 3.8 23.6 - - + +
29X VAL* 4.1 13.2 - - + -
32X ALA 3.5 3.8 - - - -
89X GLN* 1.3 75.5 - - - +
91X SER* 1.3 56.9 + - - +
92X TYR* 2.9 11.3 + - - +
93X SER* 2.8 33.1 + - - +
95X PRO 2.8 28.2 - - - +
96X TRP* 3.3 18.0 - - - +
97X THR* 3.1 32.4 + - - +
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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