Contacts of the strand formed by residues 86 - 94 (chain A) in PDB entry 2EE3
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 SER 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ARG* 5.8 0.4 - - - +
78A THR* 4.7 6.3 - - - +
79A CYS 3.6 11.9 - - - -
80A LEU* 3.7 25.2 - - - +
81A TYR* 3.4 11.5 - - - -
85A GLY* 1.3 76.4 - - - -
87A SER* 1.3 67.1 + - - +
88A THR* 5.2 0.7 + - - -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 4.9 19.8 - - - +
33A ARG* 4.7 4.9 + - - -
77A VAL 4.3 0.9 - - - -
78A THR* 3.3 5.5 - - - +
79A CYS* 3.1 30.1 + - - -
81A TYR* 2.6 35.0 + - - -
86A SER* 1.3 74.2 + - - +
88A THR* 1.3 69.5 + - - +
89A LEU* 5.4 1.1 - - - -
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 5.3 5.5 - - - +
11A PRO* 5.6 2.2 - - - +
76A ARG* 3.5 50.4 + - + +
77A VAL 3.5 2.2 - - - -
78A THR* 3.8 22.0 - - - +
86A SER* 5.2 0.5 + - - -
87A SER* 1.3 82.8 + - - +
89A LEU* 1.3 61.7 + - - +
90A THR* 3.4 12.5 + - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.7 18.6 - - + -
11A PRO* 4.0 20.0 - - + -
12A ARG* 2.9 39.9 - - + +
13A HIS* 4.8 0.7 - - - +
14A LEU* 3.2 26.5 - - + +
28A TRP* 4.1 31.6 - - + -
31A ALA* 6.0 5.4 - - + +
76A ARG* 3.2 4.2 - - - -
77A VAL* 3.0 43.2 + - + +
79A CYS* 5.5 6.1 - - - -
87A SER* 5.4 1.3 - - - -
88A THR* 1.3 68.9 - - - +
90A THR* 1.3 63.4 + - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 5.4 7.1 - - + +
14A LEU* 3.2 9.8 - - - +
74A THR* 5.4 5.4 - - - -
75A VAL 3.3 5.4 - - - -
76A ARG* 3.8 23.1 - - + +
88A THR* 3.4 13.4 + - + +
89A LEU* 1.3 73.7 - - - +
91A GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.5 15.5 - - - +
16A PHE* 3.4 13.9 - - - -
73A TYR 3.6 0.3 - - - +
74A THR* 4.7 1.4 - - - +
75A VAL* 2.6 47.8 + - - +
90A THR* 1.3 75.7 - - - +
92A ARG* 1.3 62.0 + - - +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.3 14.0 - - - -
45A SER* 5.3 4.5 + - - -
72A THR* 4.2 22.6 - - + +
73A TYR 3.7 3.6 - - - -
74A THR* 4.5 22.2 - - + +
91A GLY* 1.3 75.0 - - - +
93A VAL* 1.3 60.0 - - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.6 47.1 - - + -
19A VAL* 4.0 25.6 - - + -
24A ALA* 4.4 13.5 - - + -
67A LEU* 5.6 0.7 - - + -
71A THR 3.8 0.3 - - - +
72A THR* 3.5 2.4 - - - +
73A TYR* 2.9 48.2 + - + +
75A VAL* 4.1 7.4 - - + -
92A ARG* 1.3 76.6 - - - +
94A THR* 1.3 64.3 + - - +
95A THR* 3.6 3.5 + - + +
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.0 8.8 - - - +
70A SER* 4.4 17.7 - - - +
71A THR 3.8 4.0 - - - +
72A THR* 3.4 20.3 + - - +
93A VAL* 1.3 76.4 - - - +
95A THR* 1.3 73.8 + - - +
96A LYS* 3.8 1.2 + - - +
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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