Contacts of the strand formed by residues 61 - 65 (chain A) in PDB entry 1EG4
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 TRP 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL* 3.5 23.5 - - + +
58A GLN* 3.0 22.9 + - - +
59A GLY 3.8 5.4 - - - +
60A PRO* 1.3 93.9 - - + +
62A GLU* 1.3 63.0 + - - +
73A TYR* 3.7 37.2 - - + -
74A ILE 3.1 18.6 - - - -
75A ASN* 3.3 38.3 - - + +
76A HIS* 5.1 0.6 - - - -
80A THR* 5.3 2.9 - - - -
81A THR 6.0 0.4 - - - -
82A CYS* 4.9 11.4 - - + -
84A ASP 5.0 0.9 - - - -
86A PRO* 3.6 40.0 - - + +
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Residues in contact with GLU 62 (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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57A VAL* 3.7 5.2 - - - -
61A TRP* 1.3 78.3 - - - +
63A ARG* 1.3 72.9 + - - +
64A ALA* 3.8 1.2 + - - +
73A TYR* 3.6 2.2 - - - -
74A ILE* 2.7 55.7 + - + +
76A HIS* 2.6 43.8 + - + +
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Residues in contact with ARG 63 (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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49A SER* 4.9 2.6 + - - -
50A GLN* 2.6 55.7 + - - +
53A LEU* 3.3 49.9 - - - +
54A SER* 4.0 11.8 + - - +
56A SER* 4.2 0.4 - - - -
57A VAL* 3.6 12.1 - - + +
62A GLU* 1.3 83.9 - - - +
64A ALA* 1.3 62.9 + - - +
65A ILE* 3.1 18.8 - - - +
71A PRO* 3.4 26.8 - - + +
72A TYR 3.7 5.8 - - - +
73A TYR* 3.7 22.7 + - + -
151A ILE* 4.5 3.0 - - - +
176A ASP* 2.9 37.1 + - - -
179A LEU* 4.3 4.2 - - - +
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Residues in contact with ALA 64 (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 GLN* 4.0 4.9 - - - +
62A GLU* 5.6 1.6 - - + +
63A ARG* 1.3 76.5 - - - +
65A ILE* 1.3 66.3 + - - +
71A PRO* 3.4 5.7 - - - +
72A TYR* 2.9 53.2 + - + +
74A ILE* 3.6 27.6 - - + -
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Residues in contact with ILE 65 (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 PRO* 4.0 27.1 - - + -
49A SER* 5.8 1.6 - - - +
50A GLN* 3.4 29.1 - - + +
63A ARG* 3.1 32.8 - - - +
64A ALA* 1.3 79.3 - - - +
66A SER* 1.3 76.6 + - - +
67A PRO* 3.9 2.1 - - - +
69A LYS* 3.7 25.6 - - + +
70A VAL 3.6 2.0 - - - -
71A PRO* 4.3 9.2 - - + -
72A TYR* 3.8 7.0 + - - -
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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