Contacts of the strand formed by residues 2 - 10 (chain A) in PDB entry 1UFY
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 VAL 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 91.4 - - - +
3A ARG* 1.3 80.0 + - - +
4A GLY 4.6 0.2 - - - +
43A ALA* 5.3 5.2 - - + -
93A LEU* 4.0 23.8 - - + -
94A TRP 3.3 21.3 - - - +
95A ASN* 3.5 19.5 - - - +
96A THR 4.7 0.2 - - - -
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Residues in contact with ARG 3 (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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1A MET* 3.5 23.0 - - + +
2A VAL* 1.3 82.3 + - - +
4A GLY* 1.3 63.3 + - - +
94A TRP* 2.9 37.0 + - + +
96A THR* 3.6 21.5 - - + -
97A ASP 5.5 0.4 + - - -
98A THR 2.9 27.0 + - - +
99A PRO* 4.2 3.6 - - - +
100A GLN* 3.6 49.1 - - - +
103A VAL* 3.9 24.0 - - + -
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Residues in contact with GLY 4 (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 VAL* 4.3 1.8 - - - +
3A ARG* 1.3 76.1 - - - +
5A ILE* 1.3 60.5 + - - -
6A ARG 4.2 0.2 - - - -
91A LEU* 4.0 15.3 - - - -
92A ALA 3.2 8.7 - - - -
93A LEU* 4.3 8.2 - - - +
103A VAL* 3.6 8.8 - - - +
105A HIS* 3.5 16.7 - - - -
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Residues in contact with ILE 5 (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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4A GLY* 1.3 79.6 - - - +
6A ARG* 1.3 64.0 + - - +
30A MET* 3.4 30.9 - - + +
31A LEU* 5.7 1.1 - - + -
34A ASN* 3.6 13.7 - - - +
36A ILE* 3.8 21.8 - - + -
42A LEU* 5.2 0.2 - - + -
91A LEU* 3.4 5.3 - - - +
92A ALA* 2.8 48.8 + - + +
94A TRP* 3.7 38.8 - - + -
103A VAL* 4.0 5.4 - - + -
104A ARG 3.4 25.8 - - - +
105A HIS* 3.8 2.7 - - - +
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Residues in contact with ARG 6 (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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4A GLY 4.2 0.4 - - - -
5A ILE* 1.3 74.8 - - - +
7A GLY* 1.3 77.9 + - - +
8A ALA* 3.9 1.4 - - - +
30A MET* 3.7 6.0 - - - +
89A ARG* 3.5 21.3 - - - +
90A VAL 2.9 21.6 + - - +
91A LEU* 4.0 23.3 - - + -
105A HIS* 2.9 27.0 + - + +
106A VAL 3.0 22.7 + - - -
107A TYR* 3.4 27.1 + - + +
115A ARG* 5.7 2.2 - - - +
201A MLI 3.0 50.8 + - - +
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Residues in contact with GLY 7 (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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6A ARG* 1.3 87.8 + - - +
8A ALA* 1.3 60.4 + - - -
26A LEU* 3.8 6.3 - - - -
30A MET* 3.6 20.4 - - - +
90A VAL 2.9 28.8 + - - -
106A VAL 3.0 13.0 - - - -
107A TYR* 4.7 2.0 - - - -
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Residues in contact with ALA 8 (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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6A ARG* 3.9 5.8 - - - +
7A GLY* 1.3 76.8 - - - +
9A ILE* 1.3 63.0 + - - +
26A LEU* 3.6 7.1 - - - +
87A VAL* 4.1 5.6 - - + -
88A ILE 3.2 11.4 - - - +
89A ARG* 4.2 0.9 - - + -
106A VAL 3.0 7.7 + - - +
107A TYR* 3.4 27.4 - - + -
108A LEU 2.9 25.5 + - - -
111A ALA* 3.7 10.8 - - + -
114A LEU* 4.0 9.0 - - + -
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Residues in contact with ILE 9 (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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8A ALA* 1.3 76.7 - - - +
10A THR* 1.3 74.1 + - - +
22A ALA* 3.6 41.5 - - + +
23A THR 4.7 0.2 - - - +
25A GLU* 4.4 5.8 - - - -
26A LEU* 3.8 15.9 - - + -
87A VAL* 3.5 3.0 - - - -
88A ILE* 2.9 45.1 + - + +
108A LEU* 3.7 35.9 - - + -
109A ARG* 3.7 32.8 - - + +
111A ALA* 3.9 1.8 - - - -
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Residues in contact with THR 10 (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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9A ILE* 1.3 80.4 - - - +
11A VAL* 1.3 69.2 + - - +
84A LEU* 3.6 31.6 - - + -
85A PRO 3.9 9.0 - - - +
86A ARG 3.2 11.7 - - - +
87A VAL* 4.0 4.3 - - + -
108A LEU 3.9 1.8 + - - -
109A ARG* 3.2 32.4 + - - +
110A GLU* 3.1 33.7 + - + +
111A ALA* 3.8 8.5 - - + +
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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