Contacts of the strand formed by residues 89 - 97 (chain A) in PDB entry 1EAG
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 SER 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLN* 4.1 12.7 + - - -
81A LYS* 3.9 24.3 + - - -
82A ILE 3.0 20.0 - - - -
83A GLY* 4.1 4.0 - - - -
84A TYR* 4.7 0.9 - - - -
87A GLY 3.6 6.1 + - - -
88A SER* 1.3 76.4 - - - +
90A SER* 1.3 61.3 + - - +
91A GLN* 5.6 1.0 - - - +
117A THR* 3.2 18.7 + - - -
118A SER* 3.6 14.8 + - - -
119A ILE* 4.1 4.0 - - - +
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Residues in contact with SER 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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39A TRP* 3.2 22.5 + - - -
80A PHE* 4.6 1.1 - - - -
81A LYS* 3.4 6.0 - - - +
82A ILE* 2.9 45.4 + - - +
89A SER* 1.3 72.4 + - - +
91A GLN* 1.3 62.9 + - - +
114A VAL* 3.8 24.0 - - - -
116A SER 3.6 6.7 - - - -
117A THR* 2.9 18.9 + - - -
119A ILE* 3.9 2.6 - - - +
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Residues in contact with GLN 91 (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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48A GLN* 5.4 3.1 - - - +
80A PHE* 3.2 11.4 - - - +
81A LYS* 3.0 35.4 - - + +
89A SER* 5.6 1.1 - - - +
90A SER* 1.3 77.1 - - - +
92A GLY* 1.3 59.4 + - - +
114A VAL* 3.6 5.5 - - - +
115A ASP* 3.0 23.1 + - + +
116A SER* 3.1 36.9 + - - +
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Residues in contact with GLY 92 (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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79A PRO* 3.7 2.6 - - - +
80A PHE* 2.8 38.6 + - - +
91A GLN* 1.3 76.5 - - - +
93A THR* 1.3 63.6 + - - +
113A ASP 3.0 16.2 - - - -
114A VAL* 3.9 3.4 - - - -
115A ASP* 3.8 11.7 - - - -
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Residues in contact with THR 93 (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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75A ASP* 4.9 5.3 + - - -
77A ASN* 5.8 1.3 - - - -
78A THR 3.2 16.2 - - - +
79A PRO* 4.7 5.6 - - + -
80A PHE* 4.2 3.1 - - - +
92A GLY* 1.3 77.7 - - - +
94A LEU* 1.3 65.3 + - - +
95A TYR* 3.2 26.7 + - - -
113A ASP* 2.9 33.1 + - - -
115A ASP* 4.2 12.3 + - - +
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Residues in contact with LEU 94 (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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38A LEU 5.7 0.4 - - - +
75A ASP* 3.8 4.0 - - - +
76A LEU* 3.1 35.8 + - + +
77A ASN 4.0 1.6 + - - -
78A THR* 2.8 34.8 + - + +
79A PRO 4.8 2.0 - - - +
80A PHE* 4.1 17.9 - - + +
93A THR* 1.3 72.2 - - - +
95A TYR* 1.3 64.3 + - - +
110A VAL* 3.8 20.2 - - + -
111A LEU* 3.5 22.9 - - - +
112A ALA* 3.9 12.1 - - + +
134A GLY* 3.1 34.8 - - - +
137A TYR* 4.9 4.9 - - + +
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Residues in contact with TYR 95 (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 TYR* 4.4 10.5 - + - +
67A PRO* 3.5 36.9 - - + +
73A SER* 4.6 1.3 - - - -
74A GLN 3.2 13.7 - - - -
75A ASP* 3.5 43.8 + - + +
76A LEU* 3.6 9.8 - - - +
93A THR* 3.2 30.9 + - - -
94A LEU* 1.3 81.0 - - - +
96A LYS* 1.3 64.2 + - - +
110A VAL* 3.1 7.4 - - - +
111A LEU* 2.9 36.5 + - + +
113A ASP* 3.6 24.2 + - + -
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Residues in contact with LYS 96 (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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72A ALA 3.8 1.2 - - - +
73A SER* 3.3 0.9 - - - -
74A GLN* 2.7 74.1 + - + +
76A LEU* 4.0 14.9 - - + +
95A TYR* 1.3 81.1 - - - +
97A ASP* 1.3 65.3 - - - +
108A ASN* 3.8 32.1 - - + +
109A GLN 3.0 2.7 - - - +
110A VAL* 3.8 25.6 - - + -
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Residues in contact with ASP 97 (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 VAL* 4.4 7.2 - - + -
21A GLY* 3.4 14.6 - - - -
65A TYR* 2.7 28.7 + - - +
70A SER* 3.0 35.9 + - - -
72A ALA* 3.8 7.5 - - - +
73A SER* 3.2 12.0 + - - -
96A LYS* 1.3 77.1 - - - +
98A THR* 1.3 85.2 + - - +
99A VAL* 4.6 1.3 - - - -
106A ILE 4.0 0.2 - - - +
108A ASN* 3.5 6.6 + - - +
109A GLN* 2.5 46.4 + - - +
111A LEU* 4.4 4.5 - - + -
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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