Contacts of the strand formed by residues 93 - 102 (chain A) in PDB entry 1Y7M
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 GLY 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A THR* 1.3 76.5 - - - +
94A GLU* 1.3 65.0 + - - -
95A PHE* 3.5 9.4 - - - -
161A THR* 3.6 3.8 - - - -
162A ILE 2.9 35.5 + - - -
164B ARG* 6.0 2.5 - - - -
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Residues in contact with GLU 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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7A LYS* 5.1 8.5 + - - -
57A HIS* 4.8 3.5 + - - -
93A GLY* 1.3 73.6 - - - -
95A PHE* 1.3 71.4 + - - +
96A TYR* 5.1 12.8 - - + +
116A SER* 4.6 0.5 + - - -
159A ARG* 5.2 6.8 - - - +
160A VAL 3.8 2.8 + - - +
161A THR* 2.7 41.7 + - - +
93B GLY* 5.1 12.1 - - - -
94B GLU* 5.4 12.8 - - - +
163B ASN* 5.7 5.4 - - - +
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Residues in contact with PHE 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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7A LYS* 6.4 0.2 - - - -
91A PRO* 3.7 26.9 - - + -
92A THR 3.7 15.3 - - - -
93A GLY* 3.5 24.5 - - - -
94A GLU* 1.3 79.9 - - - +
96A TYR* 1.3 78.4 + - - +
115A LEU* 4.4 11.9 - - + -
116A SER* 3.2 21.5 - - - +
117A ALA* 3.8 30.3 - - + -
159A ARG* 3.6 1.4 - - - +
160A VAL* 2.8 40.2 + - + +
162A ILE* 3.5 29.8 - - + -
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Residues in contact with TYR 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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2A LEU* 4.0 20.9 - - + -
3A THR 4.8 8.0 + - - -
4A TYR* 5.1 7.8 - + - -
19A PHE* 3.9 23.6 - + - -
51A PRO* 3.7 24.1 - - + +
52A TYR* 5.1 7.5 + + - -
94A GLU* 5.1 11.5 - - + +
95A PHE* 1.3 84.8 - - - +
97A ILE* 1.3 65.9 + - - +
98A ILE* 3.5 12.6 + - + +
115A LEU* 3.3 10.4 - - - +
116A SER* 2.8 37.4 + - - +
157A GLY* 3.6 20.6 - - - +
158A THR 3.3 6.3 - - - +
159A ARG* 3.8 18.7 - - + -
160A VAL* 4.5 0.7 - - - -
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Residues in contact with ILE 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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48A LEU* 4.1 0.7 - - - +
58A ILE* 4.0 10.3 - - + -
96A TYR* 1.3 71.7 - - - +
98A ILE* 1.3 64.1 + - - +
99A ASN 4.1 5.8 - - - +
100A ARG* 3.8 26.0 - - - +
113A LEU* 4.1 24.0 - - + -
114A SER 3.4 7.0 - - - +
115A LEU* 4.6 2.9 - - + -
122A ILE* 3.9 28.0 - - + -
150A LEU* 5.4 0.4 - - + -
154A VAL* 4.4 9.2 - - + -
155A PRO 4.2 7.9 - - - +
156A ASN* 3.5 7.9 - - - +
157A GLY* 2.7 30.0 + - - -
158A THR* 2.9 30.2 + - - +
160A VAL* 3.8 12.3 - - + -
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Residues in contact with ILE 98 (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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18A ASP 4.2 4.5 - - - +
19A PHE* 3.3 57.0 - - + +
20A ARG* 3.9 12.3 - - + -
48A LEU* 3.9 22.8 - - + +
96A TYR* 3.9 5.6 - - + +
97A ILE* 1.3 77.9 - - - +
99A ASN* 1.3 64.6 + - - +
114A SER* 2.8 17.7 + - - +
115A LEU 3.8 3.8 - - - +
116A SER* 3.6 35.9 - - - +
156A ASN* 3.2 24.5 + - - +
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Residues in contact with ASN 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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20A ARG* 3.3 32.6 + - - +
97A ILE* 4.1 3.6 - - - +
98A ILE* 1.3 86.0 + - - +
100A ARG* 1.3 67.0 + - - +
112A TRP* 5.4 1.1 - - + -
113A LEU* 3.2 6.9 - - - +
114A SER* 2.9 39.4 + - - +
156A ASN* 3.9 11.2 + - - +
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Residues in contact with ARG 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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97A ILE* 3.8 12.9 - - - +
99A ASN* 1.3 77.9 + - - +
101A GLN* 1.3 65.0 + - - +
111A TYR* 3.8 23.6 - - + +
112A TRP* 3.0 16.2 - - - +
113A LEU* 3.7 16.9 - - + +
114A SER 4.8 0.2 - - - +
151A ALA* 2.6 39.4 + - - +
154A VAL 2.7 24.8 + - - -
155A PRO* 3.4 2.3 - - - -
156A ASN* 3.0 41.6 + - - +
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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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100A ARG* 1.3 77.8 - - - +
102A ARG* 1.3 71.1 + - - +
104A PRO* 3.5 22.5 - - + +
111A TYR* 3.2 5.1 - - - -
112A TRP* 2.8 47.9 + - + +
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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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101A GLN* 1.3 81.3 + - - +
103A ASN* 1.3 83.1 + - + +
104A PRO 3.3 0.7 - - - -
110A ALA 4.2 1.3 - - - +
111A TYR* 3.4 43.8 + - + -
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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