Contacts of the strand formed by residues 103 - 109 (chain A) in PDB entry 2EFP
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 PHE 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A SER* 3.3 4.7 - - - -
69A VAL* 2.8 35.5 + - + -
78A HIS* 3.2 37.5 - + + -
81A LEU* 3.9 29.2 - - + -
82A GLY* 3.5 18.4 - - - -
85A LEU* 4.0 17.0 - - + -
94A VAL* 3.9 17.0 - - + -
95A TYR 3.0 15.9 - - - +
96A PHE* 3.9 30.1 - + + -
101A ASN* 4.3 1.0 - - - +
102A ASP* 1.3 88.3 - - + +
104A ILE* 1.3 67.3 + - - +
105A VAL* 4.1 4.9 - - + -
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Residues in contact with ILE 104 (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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66A ILE* 3.8 25.8 - - + -
67A THR 3.4 1.8 - - - +
68A SER* 3.3 27.6 - - - +
94A VAL* 3.5 2.9 - - - -
95A TYR* 2.9 46.7 + - + +
97A VAL* 4.0 24.7 - - + -
101A ASN* 4.4 13.0 - - + +
103A PHE* 1.3 80.4 - - - +
105A VAL* 1.3 62.2 + - - +
106A MET* 4.4 11.4 - - - -
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Residues in contact with VAL 105 (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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65A VAL* 3.6 2.1 - - - +
66A ILE* 3.4 5.2 - - - -
67A THR* 2.7 49.6 + - - +
69A VAL* 4.0 12.3 - - + -
85A LEU* 4.0 34.8 - - + +
91A VAL* 3.6 28.7 - - + -
93A GLY 3.3 3.6 - - - +
94A VAL* 4.7 3.6 - - + -
103A PHE* 4.6 2.7 - - + -
104A ILE* 1.3 78.0 - - - +
106A MET* 1.3 67.0 + - - +
107A ALA* 4.0 1.0 + - + +
119A PHE* 3.7 24.5 - - + -
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Residues in contact with MET 106 (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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64A ILE* 6.6 0.4 - - + -
65A VAL 3.7 3.1 - - - +
66A ILE* 4.0 44.0 - - + -
91A VAL* 3.4 4.9 - - - +
92A TRP* 3.0 70.6 + - + -
93A GLY* 2.8 14.5 + - - +
95A TYR* 3.8 27.4 - - + +
104A ILE* 4.4 8.7 - - - -
105A VAL* 1.3 73.0 - - - +
107A ALA* 1.3 60.9 + - - +
143A GLU* 5.6 1.3 - - - +
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Residues in contact with ALA 107 (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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64A ILE* 3.7 4.9 - - - +
65A VAL* 3.0 43.3 + - + +
90A GLY 3.2 13.2 - - - +
91A VAL* 4.0 10.8 - - + -
92A TRP* 4.2 1.8 + - - +
105A VAL* 4.0 0.9 + - + -
106A MET* 1.3 75.6 - - - +
108A ARG* 1.3 68.2 + - - +
109A TYR* 3.6 26.0 - - + +
119A PHE* 4.4 7.4 - - + -
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Residues in contact with ARG 108 (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 PRO* 4.3 18.3 - - - +
61A LEU* 4.0 34.8 - - + +
63A TYR 3.6 5.4 - - - -
64A ILE* 3.9 24.8 - - + +
90A GLY* 3.0 15.4 + - - +
92A TRP* 3.6 42.6 - - + +
107A ALA* 1.3 79.8 - - - +
109A TYR* 1.3 80.3 + - - +
114A GLU* 4.8 0.2 - - - +
140A ILE* 6.1 1.8 - - - +
143A GLU* 3.3 29.5 + - - -
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Residues in contact with TYR 109 (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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61A LEU* 3.4 8.5 - - - -
62A ASP 3.1 6.1 + - - -
63A TYR* 2.7 40.6 + - - +
65A VAL* 4.9 0.7 - - + -
88A ILE* 3.9 1.4 - - - +
89A PRO 2.7 29.7 + - - -
90A GLY* 3.7 12.3 - - - -
91A VAL 3.9 0.9 + - - -
107A ALA* 3.6 18.8 - - + +
108A ARG* 1.3 87.0 - - - +
110A LYS* 1.3 58.4 + - - +
111A THR 3.4 16.8 - - - +
114A GLU* 3.6 25.1 - - + +
115A PHE* 3.8 27.6 - + + +
118A LYS* 3.9 18.2 - - + -
119A PHE* 3.3 41.0 - - + +
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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