Contacts of the strand formed by residues 44 - 49 (chain A) in PDB entry 1CEC
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 HIS 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER 3.8 5.4 - - - +
4A PHE* 3.5 31.4 - + + -
5A LYS 3.8 0.2 - - - -
7A GLY* 3.1 47.4 - - - -
8A ILE* 3.4 4.7 + - - +
42A PHE* 3.6 4.3 - - - +
43A ASP* 1.3 100.8 + - - +
45A VAL* 1.3 82.0 + - - +
83A LEU* 4.2 5.0 - - - +
84A GLY* 3.2 25.1 - - - +
86A VAL* 3.9 13.0 - - + -
277A TYR* 2.7 29.7 + + - -
310A GLY 3.6 8.5 + - - -
311A ALA* 4.1 1.2 - - - +
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Residues in contact with VAL 45 (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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8A ILE* 3.2 12.3 - - + +
10A LEU* 4.0 22.9 - - + -
34A ILE* 4.1 10.8 - - + -
37A ILE* 3.9 36.6 - - + -
44A HIS* 1.3 87.0 - - - +
46A ARG* 1.3 60.7 + - - +
47A LEU* 5.2 0.2 - - + -
74A CYS* 4.6 2.2 - - - -
78A CYS* 3.9 24.2 - - - -
83A LEU* 4.2 6.5 - - + -
84A GLY 3.1 3.4 + - - +
85A LEU* 3.4 10.4 - - + -
86A VAL 3.0 23.0 + - - -
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Residues in contact with ARG 46 (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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8A ILE 3.0 5.9 + - - -
9A ASN* 2.7 39.8 + - - +
10A LEU* 3.1 27.7 + - - +
44A HIS* 4.5 0.4 - - - -
45A VAL* 1.3 74.1 - - - +
47A LEU* 1.3 61.4 + - - +
48A PRO* 3.5 3.6 - - + +
86A VAL* 3.4 12.8 - - + +
88A ASP* 3.2 19.7 + - + +
136A GLU* 2.9 28.1 + - - +
139A ASN* 2.8 39.2 + - - +
198A HIS* 3.2 13.5 + - - -
277A TYR* 4.0 15.5 - - - +
279A GLY* 3.3 24.8 + - - -
280A GLU* 3.0 24.2 + - - +
311A ALA* 4.1 9.6 - - + -
313A TRP* 4.4 3.2 - - - -
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Residues in contact with LEU 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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10A LEU* 3.9 21.1 - - + +
13A TRP* 3.2 34.5 - - + -
14A ILE* 4.1 24.7 - - + -
45A VAL* 4.0 0.6 - - + -
46A ARG* 1.3 74.6 - - - +
48A PRO* 1.3 64.5 - - - +
49A PHE 3.7 0.2 + - - -
71A ILE* 4.6 8.1 - - - -
74A CYS* 4.1 26.0 - - + -
85A LEU* 4.1 16.6 - - + -
86A VAL 2.8 12.9 + - - +
87A LEU* 3.8 19.8 - - + +
88A ASP* 2.8 25.2 + - - +
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Residues in contact with PRO 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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9A ASN* 4.2 8.5 - - - +
10A LEU 3.8 12.1 - - - +
11A GLY* 3.9 22.2 - - - -
14A ILE* 3.6 12.6 + - - +
15A SER* 3.2 26.0 + - - +
16A GLN* 5.9 0.4 - - - +
46A ARG* 3.5 12.6 - - + +
47A LEU* 1.3 87.2 - - - +
49A PHE* 1.3 59.8 + - - +
88A ASP* 3.1 26.0 - - - +
90A HIS* 4.2 10.5 - - + +
139A ASN* 5.2 0.2 - - - +
280A GLU* 6.0 0.2 - - - +
313A TRP* 4.4 12.1 - - + -
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Residues in contact with PHE 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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14A ILE* 3.5 31.4 - - + +
15A SER* 3.8 0.4 - - - -
47A LEU 4.8 0.4 - - - +
48A PRO* 1.3 75.4 - - - +
50A ASP* 1.3 77.5 + - - +
51A TYR* 4.8 3.6 - - - -
53A ILE* 4.9 1.6 - - + -
54A ILE* 3.9 26.5 - - + -
71A ILE* 4.5 2.7 - - + -
87A LEU* 3.6 33.2 - - + -
88A ASP 2.8 25.1 + - - -
89A MET* 3.6 53.1 - - + +
90A HIS 2.8 23.4 + - - -
118A ILE* 4.8 2.9 - - + -
119A TRP* 4.2 5.4 - + - -
122A LEU* 4.0 16.6 - - + -
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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