Contacts of the strand formed by residues 46 - 57 (chain A) in PDB entry 2CE6
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 VAL 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PRO* 1.3 73.7 - - - +
47A VAL* 1.3 69.4 + - - +
48A LEU* 4.3 2.2 + - + -
96A ILE 3.7 1.0 - - - +
97A SER* 3.3 3.3 - - - -
98A ILE* 2.8 44.2 + - + +
100A ASN* 3.8 32.3 - - + +
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Residues in contact with VAL 47 (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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37A PHE* 4.3 6.5 - - + -
45A PRO* 3.8 3.3 + - + -
46A VAL* 1.3 86.6 - - - +
48A LEU* 1.3 65.1 + - - +
49A LEU* 3.8 24.2 - - + -
68A LEU* 3.6 26.0 - - + +
71A VAL* 3.8 38.8 - - + +
76A PHE* 4.4 12.1 - - + -
95A TRP* 4.4 6.7 - - + -
96A ILE 3.2 12.3 - - - +
97A SER* 4.1 14.6 - - - -
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Residues in contact with LEU 48 (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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46A VAL* 4.3 2.6 + - + -
47A VAL* 1.3 76.1 - - - +
49A LEU* 1.3 77.6 - - - +
50A SER* 5.6 4.9 - - - -
95A TRP* 3.1 28.1 - - - +
96A ILE* 3.0 36.4 + - + +
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Residues in contact with LEU 49 (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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47A VAL* 3.8 19.7 + - + -
48A LEU* 1.3 97.2 - - - +
50A SER* 1.3 60.7 + - - +
51A ILE 4.4 0.2 - - - -
66A ALA* 3.9 21.7 - - + +
67A ARG 3.7 10.1 - - - +
68A LEU* 3.7 44.5 - - + +
76A PHE* 4.5 7.0 - - + -
78A ALA* 3.9 8.5 - - + -
93A ILE* 3.6 20.0 - - + -
94A SER 3.5 2.0 - - - -
95A TRP* 3.8 12.3 - - + -
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Residues in contact with SER 50 (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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48A LEU* 5.6 5.8 - - - -
49A LEU* 1.3 74.6 - - - +
51A ILE* 1.3 65.8 + - - +
52A THR* 3.3 17.0 + - - +
93A ILE* 3.2 4.8 - - - +
94A SER* 2.6 45.3 + - - -
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Residues in contact with ILE 51 (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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50A SER* 1.3 73.1 + - - +
52A THR* 1.3 62.5 + - - +
53A GLN 3.6 21.8 - - - +
54A LEU* 3.9 21.8 - - + -
64A VAL* 4.1 17.9 - - + -
65A ILE* 5.3 0.2 - - - -
66A ALA* 3.7 30.0 - - + +
91A MET* 3.7 25.4 - - + -
92A SER 3.4 7.2 - - - +
93A ILE* 4.3 1.6 - - + +
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Residues in contact with THR 52 (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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6A LYS* 4.3 14.0 + - - -
50A SER* 3.3 17.7 + - - +
51A ILE* 1.3 77.0 - - - +
53A GLN* 1.3 62.6 + - - +
92A SER* 2.9 12.3 + - - -
94A SER* 2.9 34.9 + - - +
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Residues in contact with GLN 53 (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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6A LYS* 4.8 7.5 + - - +
8A ASN* 4.6 3.2 + - - +
51A ILE* 3.6 6.9 - - - +
52A THR* 1.3 82.9 - - - +
54A LEU* 1.3 74.1 + - - +
55A ASP* 5.9 0.2 - - + -
90A SER* 3.0 33.0 + - - +
91A MET* 3.2 5.1 - - - -
92A SER* 3.1 48.3 + - - +
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Residues in contact with LEU 54 (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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51A ILE* 3.9 18.2 - - + -
53A GLN* 1.3 84.2 - - - +
55A ASP* 1.3 62.7 + - - +
56A VAL* 3.6 27.4 - - + -
62A LEU* 4.9 14.1 - - + -
64A VAL* 4.1 27.4 - - + -
88A VAL* 5.3 0.9 - - + -
90A SER* 3.5 10.1 - - - +
91A MET* 4.5 11.0 - - + -
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Residues in contact with ASP 55 (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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54A LEU* 1.3 77.7 - - - +
56A VAL* 1.3 59.2 + - - +
88A VAL* 3.5 2.6 - - - -
89A TYR* 2.6 59.0 + - - +
90A SER* 3.0 28.8 + - - +
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Residues in contact with VAL 56 (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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54A LEU* 3.6 29.3 - - + -
55A ASP* 1.3 82.1 + - - +
57A GLU* 1.3 77.7 + - - +
58A GLN* 3.5 4.0 + - - +
60A GLN 5.0 0.2 - - - +
61A ASN 4.8 0.7 - - - +
62A LEU* 4.2 39.7 - - + -
64A VAL* 4.6 1.6 - - + -
86A THR* 4.6 7.2 - - + -
87A LYS 3.5 8.5 - - - +
88A VAL* 4.0 16.2 - - + -
89A TYR* 4.0 4.6 - - - -
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Residues in contact with GLU 57 (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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56A VAL* 1.3 80.5 - - - +
58A GLN* 1.3 66.7 + - - +
59A SER* 2.8 37.3 + - - +
60A GLN* 3.2 27.8 + - + +
61A ASN 5.0 0.2 - - - +
87A LYS* 2.8 39.8 + - + +
89A TYR* 2.4 36.2 + - - +
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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