Contacts of the strand formed by residues 87 - 95 (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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ALA* 4.1 11.2 - - + -
9A ILE 3.5 11.9 - - - +
10A THR* 4.0 2.0 - - + -
48A THR 3.8 0.5 - - - +
49A VAL* 3.5 4.9 - - - -
50A THR* 3.0 29.7 + - + +
53A LEU* 4.0 1.4 - - - +
84A LEU* 3.4 46.2 - - + +
85A PRO 3.6 7.6 - - - +
86A ARG* 1.3 74.2 - - - +
88A ILE* 1.3 72.0 + - - +
89A ARG* 3.6 39.5 + - + +
111A ALA* 4.7 1.3 - - + -
114A LEU* 4.2 4.5 - - + -
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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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8A ALA* 3.2 4.0 - - - -
9A ILE* 2.9 45.3 + - + +
11A VAL* 4.1 13.0 - - + -
19A ILE* 3.9 22.7 - - + +
22A ALA* 4.0 18.4 - - + -
23A THR* 3.8 28.5 - - + +
26A LEU* 4.1 1.3 - - + +
47A PHE* 4.7 5.6 - - + -
48A THR 3.5 8.7 - - - +
49A VAL* 4.1 8.5 - - + -
53A LEU* 4.0 13.7 - - + -
58A PRO* 4.5 15.0 - - + -
87A VAL* 1.3 74.5 - - - +
89A ARG* 1.3 67.2 + - - +
90A VAL* 4.7 5.6 - - + -
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Residues in contact with ARG 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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6A ARG* 3.5 20.0 - - - +
7A GLY 3.4 3.1 - - - -
8A ALA* 4.2 1.8 - - + -
47A PHE* 3.2 8.0 - - - +
48A THR* 2.9 47.4 + - + +
50A THR* 3.7 9.7 - - - +
77A GLU* 3.4 41.1 + - - +
83A SER* 5.9 3.8 - - - -
84A LEU* 5.3 2.6 + - - +
87A VAL* 3.6 33.6 + - + +
88A ILE* 1.3 75.1 - - - +
90A VAL* 1.3 65.2 + - - +
114A LEU* 3.6 19.8 - - - +
201A MLI 2.9 40.5 + - - +
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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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6A ARG* 2.9 13.2 + - - -
7A GLY 2.9 30.6 + - - +
23A THR* 5.5 2.0 - - + -
26A LEU* 3.6 25.1 - - + -
27A LEU* 4.0 9.4 - - + -
30A MET* 3.7 29.4 - - + -
45A VAL* 3.5 27.8 - - + -
46A ILE 3.5 3.4 - - - +
47A PHE* 3.8 18.8 - - + -
88A ILE* 4.7 4.5 - - + -
89A ARG* 1.3 78.8 - - - +
91A LEU* 1.3 62.0 + - - +
92A ALA* 4.1 2.9 - - + +
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Residues in contact with LEU 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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4A GLY* 4.0 21.8 - - - -
5A ILE 3.4 10.8 - - - +
6A ARG* 4.0 20.9 - - + -
44A ALA 4.2 0.2 - - - +
45A VAL* 3.5 1.2 - - - -
46A ILE* 2.8 59.7 + - + +
90A VAL* 1.3 73.9 - - - +
92A ALA* 1.3 59.0 + - - +
93A LEU* 3.9 20.2 + - + +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ARG 3.6 0.7 - - - +
4A GLY* 3.2 5.4 - - - -
5A ILE* 2.8 51.1 + - + +
27A LEU* 6.1 1.1 - - + -
30A MET* 4.2 13.7 - - + -
31A LEU* 6.2 1.8 - - + -
42A LEU* 4.3 15.9 - - + -
44A ALA 3.8 4.7 - - - -
45A VAL* 4.2 19.3 - - + -
90A VAL* 4.1 1.8 - - + +
91A LEU* 1.3 72.5 - - - +
93A LEU* 1.3 60.2 + - - +
94A TRP 3.7 0.4 + - - -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A VAL* 4.0 21.3 - - + -
3A ARG 3.9 1.6 - - - -
4A GLY* 4.3 8.7 - - - +
42A LEU* 3.6 5.3 - - - -
43A ALA* 2.8 42.3 + - + -
44A ALA* 2.9 31.6 + - + +
46A ILE* 4.7 14.6 - - + -
91A LEU* 4.2 25.1 - - + +
92A ALA* 1.3 74.9 - - - +
94A TRP* 1.3 55.8 + - - +
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Residues in contact with TRP 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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2A VAL* 3.3 5.1 - - - +
3A ARG* 2.9 51.6 + - + +
5A ILE* 3.7 26.9 - - + -
34A ASN* 3.5 41.7 - - + -
35A GLY 5.4 0.4 - - - -
36A ILE* 3.5 28.0 - - + +
41A GLU* 2.9 42.0 + - + -
42A LEU* 4.6 4.9 - - + -
93A LEU* 1.3 70.8 - - - +
95A ASN* 1.4 68.5 + - - +
96A THR* 3.2 35.9 + - + +
98A THR* 3.5 26.9 - - + -
103A VAL* 4.3 8.1 - - + -
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Residues in contact with ASN 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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1A MET 3.6 7.1 + - - +
2A VAL* 3.5 20.8 - - - +
40A GLU 4.6 4.9 + - - -
41A GLU* 2.9 33.1 + - - +
42A LEU 4.4 1.0 + - - -
43A ALA* 3.8 25.2 - - - +
93A LEU 4.1 0.2 + - - -
94A TRP* 1.4 76.5 + - - +
96A THR* 1.3 61.0 + - - +
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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