Contacts of the strand formed by residues 98 - 104 (chain A) in PDB entry 1EUT
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.3 20.9 - - - -
85A ASP* 3.4 5.7 - - - -
86A GLY 2.9 34.5 + - - -
96A PRO 4.3 2.8 + - - -
97A ASN* 1.3 71.9 - - - +
99A ILE* 1.3 62.8 + - - +
100A LEU* 3.8 9.8 + - - -
116A VAL* 4.9 3.3 - - - +
118A SER 3.4 9.9 - - - -
119A ALA* 3.8 5.4 - - - +
120A GLY* 3.1 22.2 + - - +
129A PHE 4.0 2.1 - - - +
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Residues in contact with ILE 99 (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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83A SER* 3.4 22.9 - - - +
84A TYR 3.8 1.1 - - - +
85A ASP* 3.4 24.9 - - - +
98A SER* 1.3 71.4 - - - +
100A LEU* 1.3 59.4 + - - +
116A VAL* 3.7 4.5 - - - +
117A VAL* 2.9 36.3 + - + -
118A SER* 2.8 22.1 + - - +
129A PHE* 3.7 22.7 - - + +
130A SER* 3.9 12.3 - - - -
132A PRO* 3.4 28.7 - - + -
145A ASN* 3.9 10.3 - - - +
147A HIS* 4.0 13.2 - - + -
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Residues in contact with LEU 100 (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 PHE* 3.9 24.0 - - + -
67A TYR* 3.9 2.0 - - + -
83A SER* 2.6 35.9 + - - -
84A TYR* 3.0 38.2 + - + +
86A GLY* 3.5 33.4 - - - +
98A SER* 4.2 6.7 - - - +
99A ILE* 1.3 76.6 - - - +
101A GLN* 1.3 61.3 + - - +
114A GLN* 3.9 23.1 - - + +
115A GLN 3.3 10.3 - - - +
116A VAL* 3.9 27.6 - - + -
117A VAL* 4.5 2.0 - - - +
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Residues in contact with GLN 101 (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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81A LEU* 3.8 17.4 - - + +
82A ALA 3.2 6.7 - - - +
84A TYR* 5.2 1.5 - - - -
100A LEU* 1.3 79.1 - - - +
102A ARG* 1.3 72.7 + - - +
103A ARG* 4.3 9.8 + - - +
113A GLU 3.6 2.4 - - - +
114A GLN* 3.7 0.8 - - - -
115A GLN* 2.7 47.8 + - + +
117A VAL* 3.8 19.8 - - + +
134A TYR* 2.6 31.7 + - - +
181A GLY 3.6 15.8 - - - +
184A TRP* 3.3 27.8 + - - -
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Residues in contact with ARG 102 (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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54A GLN* 5.6 3.0 - - - +
55A ASP 4.5 4.4 + - - -
56A LEU* 3.9 36.2 + - + +
81A LEU* 3.9 1.4 - - - -
82A ALA 2.9 32.2 + - - +
84A TYR* 3.3 29.4 - - + +
101A GLN* 1.3 77.9 - - - +
103A ARG* 1.3 59.6 + - - +
111A TRP* 3.1 46.8 + - + +
112A GLY 2.5 32.6 + - - -
113A GLU* 4.0 13.2 + - - +
114A GLN* 3.9 17.0 - - - +
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Residues in contact with ARG 103 (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 THR* 4.4 4.4 + - - +
79A ASP* 3.0 25.7 + - + +
80A LEU 3.6 8.7 - - - +
81A LEU* 3.7 23.9 - - + +
101A GLN* 4.3 7.0 + - - +
102A ARG* 1.3 74.9 - - - +
104A SER* 1.3 62.0 + - - +
105A THR* 4.0 18.1 + - + +
111A TRP* 3.4 6.0 - - - -
112A GLY* 2.6 37.0 + - - +
113A GLU 4.6 1.6 + - - -
179A ASP 4.6 0.4 + - - -
180A GLY* 2.4 34.9 + - - -
181A GLY 4.1 9.5 + - - -
182A LEU* 3.6 29.4 - - - +
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Residues in contact with SER 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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78A GLY 4.3 0.9 - - - +
79A ASP* 3.3 4.0 - - - -
80A LEU* 2.8 41.1 + - - +
103A ARG* 1.3 74.5 - - - +
105A THR* 1.3 61.6 + - - +
106A ASP* 2.9 4.9 + - - -
107A GLY 4.4 1.2 + - - -
108A GLY* 2.7 28.8 + - - -
110A THR 2.7 25.1 + - - -
111A TRP* 3.4 25.5 - - - -
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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