Contacts of the strand formed by residues 88 - 94 (chain Y) 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 ALA 88 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38Y ARG* 4.4 7.9 - - + +
39Y GLN 3.3 31.4 - - - +
40Y ALA* 3.6 4.9 - - + +
41Y PRO* 4.4 3.6 - - - -
85Y GLU 5.7 0.4 - - - +
86Y ASP 3.2 5.0 + - - +
87Y THR* 1.3 77.8 - - - +
89Y VAL* 1.3 61.7 + - - +
90Y TYR* 3.2 21.4 - - + -
108Y LEU* 3.4 8.5 - - - -
109Y VAL 2.9 30.4 + - - -
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Residues in contact with VAL 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y VAL 4.1 0.2 - - - +
38Y ARG* 3.4 2.8 - - - -
39Y GLN* 2.9 39.3 + - + +
41Y PRO* 5.5 3.1 - - + +
88Y ALA* 1.3 74.2 - - - +
90Y TYR* 1.3 62.3 + - - +
91Y TYR* 3.6 27.1 + - + +
105Y GLN 4.9 1.1 - - - +
106Y GLY* 3.6 26.9 - - - -
107Y THR 3.5 8.7 - - - +
108Y LEU* 3.8 21.1 - - + -
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Residues in contact with TYR 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y GLU* 2.6 25.5 - - - +
20Y LEU* 3.5 20.9 - - + -
36Y TRP* 4.7 6.1 - + + -
37Y VAL 3.8 2.7 - - - -
38Y ARG* 2.9 43.8 + - + -
48Y VAL* 5.0 5.2 - - + -
67Y PHE* 4.5 4.5 - + - -
80Y LEU* 4.0 20.4 - - + -
82Y MET* 3.0 29.5 - - + +
86Y ASP 2.6 29.7 + - - -
88Y ALA* 3.2 24.7 - - + -
89Y VAL* 1.3 73.8 - - - +
91Y TYR* 1.3 57.7 + - - +
106Y GLY* 3.3 0.6 - - - -
107Y THR 2.9 20.9 + - - +
109Y VAL* 3.9 18.8 - - + -
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Residues in contact with TYR 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X GLN* 4.0 3.8 + - - -
41X GLY 5.3 1.4 - - - -
42X LYS* 3.5 19.1 + - - -
43X ALA* 3.4 34.1 - - + -
44X PRO* 4.5 4.7 - - + -
6Y GLU* 3.3 4.9 - - - -
36Y TRP* 3.3 10.4 - - - -
37Y VAL 2.8 43.2 + - - +
39Y GLN* 3.8 24.3 + - + -
45Y LEU* 4.9 2.0 - - + -
89Y VAL* 3.6 29.2 - - + +
90Y TYR* 1.3 75.8 - - - +
92Y CYS* 1.3 62.0 + - - +
103Y TRP* 3.5 29.6 - + + -
104Y GLY 3.8 4.7 - - - -
105Y GLN 3.7 6.5 + - - -
106Y GLY* 3.5 25.6 - - - -
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Residues in contact with CYS 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LEU* 3.9 11.7 - - - -
6Y GLU* 2.6 27.3 + - - +
22Y CYS* 2.1 53.2 - - + -
34Y ILE* 4.1 5.2 - - + -
35Y HIS 3.2 9.2 - - - +
36Y TRP* 3.9 14.6 - - + -
91Y TYR* 1.3 75.2 - - - +
93Y SER* 1.3 63.9 + - - +
103Y TRP* 3.7 0.9 - - - -
104Y GLY 3.0 24.9 + - - -
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Residues in contact with SER 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LEU* 4.0 2.7 - - - -
34Y ILE* 3.6 3.5 - - - +
35Y HIS* 2.7 52.2 + - - +
37Y VAL* 5.5 2.7 - - - -
92Y CYS* 1.3 77.5 - - - +
94Y ARG* 1.3 59.2 + - - +
100Y PHE* 3.5 32.3 - - - +
102Y TYR 2.9 17.9 + - - -
103Y TRP* 4.1 22.2 + - - -
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Residues in contact with ARG 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y VAL* 3.3 31.0 - - + +
4Y LEU* 3.6 9.6 - - + +
27Y TYR* 3.3 51.4 - - + +
32Y TYR* 3.3 42.5 + - - -
33Y VAL 3.6 13.2 - - - +
34Y ILE* 4.5 4.5 - - + -
93Y SER* 1.3 76.6 - - - +
95Y PRO* 1.3 89.5 + - - +
96Y THR* 4.6 4.9 - - - +
102Y TYR* 2.9 60.6 + - + +
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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