Contacts of the strand formed by residues 84 - 90 (chain I) in PDB entry 4EUP
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 84 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36I ARG* 3.5 32.5 - - + -
37I GLN 3.7 9.4 - - - +
38I TYR* 3.8 13.5 - - + +
39I SER 5.5 1.3 - - - +
82I ASP 3.5 2.2 + - - -
83I SER* 1.3 77.9 - - - +
85I THR* 1.3 65.5 + - - +
86I TYR* 4.0 9.3 - - + +
105I GLN* 3.6 4.4 - - - +
106I VAL 2.9 29.2 + - - +
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Residues in contact with THR 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I TYR 3.7 0.7 - - - +
36I ARG* 3.5 1.7 - - - -
37I GLN* 2.8 46.0 + - - +
84I ALA* 1.3 77.5 + - - +
86I TYR* 1.3 64.9 + - - +
87I LEU* 3.9 9.1 + - + +
102I LYS 5.2 1.3 - - - +
103I GLY* 4.1 11.4 - - - -
104I THR 3.3 23.8 - - - +
105I GLN* 3.7 16.1 - - + +
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Residues in contact with TYR 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I GLN* 3.0 9.1 + - - -
20I LEU* 3.9 25.6 - - + -
34I TRP* 4.6 9.2 - - + -
35I TYR 3.3 2.5 - - - +
36I ARG* 3.6 40.1 + - + -
46I ILE* 3.9 19.1 - - + -
60I PHE* 5.0 2.8 - + - -
73I LEU* 4.5 3.1 - - + -
75I ILE* 3.9 20.4 - - + +
82I ASP* 2.4 42.4 + - - -
84I ALA* 4.0 9.9 - - + -
85I THR* 1.3 72.0 - - - +
87I LEU* 1.3 62.5 + - - +
103I GLY* 3.4 0.9 - - - -
104I THR 2.8 35.5 + - - +
106I VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLN* 3.8 2.9 - - - +
33I PHE 3.7 0.2 - - - +
34I TRP* 3.3 8.3 - - - -
35I TYR* 2.6 47.6 + - + +
37I GLN* 3.5 28.5 - - + +
43I PRO* 4.1 23.8 - - + -
85I THR* 4.8 7.6 - - + +
86I TYR* 1.3 75.0 - - - +
88I CYS* 1.3 60.1 + - - +
89I ALA 3.9 1.0 + - - -
100I PHE* 4.6 20.6 - - + -
101I GLY 3.6 20.9 - - - +
102I LYS 4.3 3.4 - - - +
103I GLY* 3.8 15.0 - - - +
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Residues in contact with CYS 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 3.6 5.9 - - - +
5I GLN* 3.3 24.0 + - + +
22I CYS* 2.1 50.5 - - - -
32I PHE* 6.1 0.7 - - - -
33I PHE 3.5 9.6 - - - -
34I TRP* 3.6 14.1 - - + -
71I VAL* 4.9 7.0 - - - -
87I LEU* 1.3 74.2 - - - +
89I ALA* 1.3 64.6 + - - +
90I VAL* 4.6 4.0 - - - -
100I PHE* 4.7 0.4 - - - -
101I GLY 2.8 28.3 + - - +
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Residues in contact with ALA 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I PHE* 3.8 0.5 - - - -
33I PHE* 2.9 41.3 + - + +
35I TYR* 3.8 18.4 - - + -
87I LEU 3.9 1.4 + - - -
88I CYS* 1.3 72.9 - - - +
90I VAL* 1.3 69.7 + - - +
98I LEU* 4.4 6.7 - - + -
99I THR 3.3 7.4 - - - +
100I PHE* 3.7 31.4 - - + +
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Residues in contact with VAL 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 3.9 28.9 - - + -
24I TYR* 4.2 15.5 - - + -
29I SER* 3.7 21.1 - - - +
31I SER 3.7 6.5 - - - +
32I PHE* 3.6 36.6 - - + -
33I PHE* 5.0 0.4 - - - -
88I CYS* 4.6 7.2 - - - -
89I ALA* 1.3 80.7 - - - +
91I SER* 1.3 66.2 + - - +
92I GLY 3.2 0.5 + - - -
98I LEU* 3.5 4.9 - - - -
99I THR* 2.7 39.2 + - - -
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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