Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 1EAS
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 GLN 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL 3.7 1.2 - - - +
67A VAL* 3.5 2.6 - - - -
68A VAL* 2.9 44.3 + - + +
79A THR 4.6 3.6 + - - +
80A GLU* 1.3 79.1 - - - +
82A TYR* 1.3 63.7 + - - +
83A VAL* 4.0 5.4 + - + +
112A VAL* 3.5 11.5 - - + +
113A THR* 3.0 51.4 + - - -
115A ASN* 4.1 10.5 - - - +
118A VAL* 3.6 20.2 - - - +
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Residues in contact with TYR 82 (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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34A GLN* 5.7 0.2 - - - -
65A ARG* 3.4 51.1 - - + -
66A VAL 3.5 5.8 - - - +
67A VAL* 3.5 24.0 - - + -
70A GLU* 5.1 4.4 + - - -
76A ASN* 3.7 19.3 + - - +
80A GLU* 3.6 30.7 + - + +
81A GLN* 1.3 78.0 - - - +
83A VAL* 1.3 66.0 + - - +
110A GLN* 4.6 3.6 - - - +
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Residues in contact with VAL 83 (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 ARG* 3.5 4.9 - - - +
66A VAL* 2.8 42.1 + - + +
68A VAL* 5.7 0.2 - - + -
81A GLN* 4.7 5.8 - - + +
82A TYR* 1.3 84.0 - - - +
84A GLY* 1.3 61.0 + - - +
108A LEU* 3.7 41.7 - - + -
110A GLN* 3.5 33.2 - - + +
111A SER 5.3 1.3 - - - +
112A VAL* 3.9 22.0 - - + -
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Residues in contact with GLY 84 (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 PHE* 4.2 11.4 - - - -
83A VAL* 1.3 78.1 - - - +
85A VAL* 1.3 62.4 + - - -
108A LEU* 3.6 6.1 - - - +
109A ALA* 2.8 32.0 + - - -
110A GLN* 3.6 10.5 + - - -
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Residues in contact with VAL 85 (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 PHE* 3.6 40.2 + - + +
66A VAL* 4.2 17.5 - - + -
84A GLY* 1.3 74.0 - - - -
86A GLN* 1.3 61.8 + - - +
87A LYS 3.8 11.7 - - - +
88A ILE* 3.8 31.6 - - + -
106A LEU* 3.9 28.9 - - + -
107A ARG 3.9 3.4 - - - +
108A LEU* 4.7 2.2 - - + +
109A ALA* 4.8 1.1 - - - +
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Residues in contact with GLN 86 (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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84A GLY 3.9 1.2 + - - -
85A VAL* 1.3 76.2 - - - +
87A LYS* 1.3 60.9 + - + +
107A ARG* 2.8 49.4 + - + +
108A LEU 4.0 4.8 - - - +
109A ALA* 3.8 28.5 + - + +
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Residues in contact with LYS 87 (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 TRP* 5.0 0.4 - - + -
85A VAL* 3.8 1.0 - - - +
86A GLN* 1.3 85.1 - - + +
88A ILE* 1.3 68.5 + - - +
89A VAL* 3.9 16.7 - - + +
105A LEU 3.9 0.6 - - - +
106A LEU* 3.3 4.3 - - - -
107A ARG* 2.7 53.2 + - + +
245A ASN* 3.2 47.0 + - + +
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Residues in contact with ILE 88 (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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59A VAL* 3.6 35.9 - - + +
61A ARG 5.7 1.3 - - - +
63A LEU 5.5 0.9 - - - +
65A PHE* 3.9 34.1 - - + -
85A VAL* 3.8 17.5 - - + -
86A GLN 5.8 0.2 - - - -
87A LYS* 1.3 79.8 + - - +
89A VAL* 1.3 66.0 + - - +
90A VAL* 3.9 15.1 + - + +
104A ALA* 5.0 0.2 - - + -
105A LEU 3.7 2.7 - - - -
106A LEU* 3.9 9.6 - - + -
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Residues in contact with VAL 89 (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 TRP* 4.4 9.6 - - + -
87A LYS* 3.9 26.0 - - + +
88A ILE* 1.3 75.7 - - - +
90A VAL* 1.3 69.2 + - - +
92A PRO* 5.9 2.0 - - + -
104A ALA* 3.2 3.0 - - - -
105A LEU* 2.8 43.5 + - + +
237A TRP* 3.6 13.4 - - + +
241A VAL* 4.0 34.8 - - + -
245A ASN* 4.3 4.9 - - - +
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Residues in contact with VAL 90 (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 ALA* 3.5 13.0 - - + -
59A VAL* 4.0 21.8 - - + +
60A ASP* 4.7 5.6 - - - +
88A ILE* 3.9 23.4 + - + +
89A VAL* 1.3 79.9 - - - +
91A HIS* 1.3 77.2 + - - +
92A PRO* 3.2 8.0 - - - +
94A TRP* 3.5 32.5 - - + -
103A ILE 3.9 3.4 - - - -
104A ALA* 3.9 2.2 - - + -
237A TRP* 4.0 2.9 - - - -
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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