Contacts of the strand formed by residues 43 - 49 (chain A) in PDB entry 1EQR
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 GLY 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A CYS* 3.6 8.7 - - - +
7A GLY* 3.8 6.1 - - - -
39A ARG* 3.5 5.1 - - - -
40A ASP* 2.6 38.2 + - - -
41A ARG 3.3 1.2 + - - -
42A GLU* 1.3 77.1 - - - +
44A ILE* 1.3 65.7 + - - -
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Residues in contact with ILE 44 (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 CYS 4.3 1.3 - - - -
7A GLY* 4.2 1.0 - - - -
25A ASN* 3.2 40.8 - - + +
37A ASP* 3.7 28.7 - - + +
38A MET 3.3 4.7 - - - +
39A ARG* 3.8 19.1 - - + -
43A GLY* 1.3 77.4 - - - -
45A VAL* 1.3 56.3 + - - +
87A MET* 3.4 26.8 - - + +
88A ALA 5.8 0.2 + - - -
89A THR* 2.7 31.0 + - - +
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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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6A CYS* 3.1 37.2 - - + +
9A LEU* 3.5 22.9 - - + -
20A LEU* 3.7 22.0 - - + -
37A ASP* 3.5 0.7 - - - -
38A MET* 2.8 36.3 + - + +
44A ILE* 1.3 75.9 - - - +
46A GLN* 1.3 69.9 + - - +
47A VAL* 3.6 5.5 + - + -
89A THR* 3.6 4.5 - - - +
92A ILE* 3.5 24.2 - - + -
94A VAL* 4.2 4.0 - - + -
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Residues in contact with GLN 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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26A ARG* 4.3 10.2 + - - -
28A ARG* 5.8 1.0 + - - -
35A PHE* 3.7 32.6 - - + +
36A ILE 3.4 5.6 - - - +
37A ASP* 3.8 17.3 + - - +
45A VAL* 1.3 77.2 - - - +
47A VAL* 1.3 62.6 + - - +
78A ARG* 3.5 42.0 + - - +
82A ASN* 5.9 2.6 - - - +
87A MET* 4.7 4.6 - - + +
89A THR* 4.6 2.4 + - - -
92A ILE 5.0 0.6 + - - -
93A GLU* 3.2 33.0 + - + +
94A VAL 2.9 23.0 + - - -
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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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20A LEU* 4.6 0.9 - - + -
35A PHE* 3.4 5.5 - - - -
36A ILE* 2.6 44.1 + - + +
38A MET* 3.9 35.2 - - + -
45A VAL* 4.1 9.0 - - + +
46A GLN* 1.3 80.6 - - - +
48A PHE* 1.3 63.1 + - - +
49A PHE* 3.4 31.2 - - + -
71A VAL* 4.2 12.6 - - + -
94A VAL* 3.4 18.4 - - + +
96A ALA* 3.8 14.8 - - + -
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Residues in contact with PHE 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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33A LEU* 3.3 48.9 - - + -
34A ILE 4.0 3.6 - - - -
35A PHE* 3.7 28.5 - + + -
46A GLN 4.2 0.8 + - - -
47A VAL* 1.3 71.7 - - - +
49A PHE* 1.3 79.7 + - - +
50A ASP* 3.9 11.8 + - + -
76A ARG* 3.3 35.2 - - - -
93A GLU* 4.1 13.0 - - - +
94A VAL 2.7 13.2 + - - +
95A LEU* 3.5 24.6 - - + +
96A ALA* 2.8 30.0 + - - +
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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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33A LEU* 4.2 0.7 - - - +
34A ILE* 3.0 44.9 + - + +
36A ILE* 3.8 25.8 - - + -
47A VAL* 3.4 25.8 - - + -
48A PHE* 1.3 90.4 - - - +
50A ASP* 1.3 62.5 + - - +
51A PRO* 4.1 2.9 - - - +
56A ALA* 3.8 13.7 - - + -
57A LEU* 4.6 12.8 - - + +
60A ALA* 3.5 22.2 - - + -
63A LEU* 4.2 7.0 - - + -
69A ILE* 5.6 0.2 - - + -
71A VAL* 4.9 4.3 - - + -
96A ALA* 3.9 18.4 - - + -
98A SER 5.2 0.2 - - - -
99A LEU* 3.7 40.4 - - + -
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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