Contacts of the strand formed by residues 60 - 65 (chain F) in PDB entry 1U1C
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 LYS 60 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F GLU* 3.8 4.2 - - - +
57F LEU* 2.7 37.7 + - - +
58F ASP* 3.7 19.3 + - + +
59F GLY* 1.3 81.8 - - - +
61F PRO* 1.3 71.1 - - + +
62F VAL* 3.6 2.4 + - - +
253F LEU* 3.8 52.0 + - + +
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Residues in contact with PRO 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU 3.7 16.6 - - - +
17F GLN* 3.4 32.3 - - + +
18F GLY 4.2 4.3 - - - +
19F ALA* 3.5 23.1 - - + +
20F THR 4.7 1.7 + - - -
21F LEU 4.9 1.2 + - - +
54F ARG* 4.6 7.4 - - - +
55F ALA 3.4 9.0 - - - +
56F GLU* 4.1 6.0 - - + -
59F GLY 4.2 3.8 - - - +
60F LYS* 1.3 91.7 - - + +
62F VAL* 1.3 62.2 + - - +
253F LEU* 4.8 1.9 - - - +
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA* 4.4 0.9 - - - -
21F LEU* 3.8 25.8 - - + +
23F ILE* 4.2 13.7 - - + -
38F MET* 4.1 24.5 - - + -
54F ARG* 3.5 4.8 - - - +
55F ALA* 2.7 40.0 + - - +
57F LEU* 4.0 15.5 - - + -
60F LYS 3.6 5.6 + - - +
61F PRO* 1.3 79.0 - - - +
63F ILE* 1.3 76.8 + - - +
64F VAL 4.2 0.2 + - - -
249F ALA* 5.4 0.9 - - + -
253F LEU* 3.8 25.4 - - + -
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 3.7 31.4 - - + -
19F ALA* 4.0 10.3 - - + -
21F LEU 3.0 13.0 + - - +
22F ALA* 3.1 12.8 - - + -
23F ILE 2.8 31.0 + - - -
44F LEU* 3.7 26.7 - - + -
52F THR* 4.1 9.9 - - + -
53F TRP 3.5 11.9 - - - +
54F ARG* 3.9 12.6 - - + -
62F VAL* 1.3 79.4 - - - +
64F VAL* 1.3 68.1 + - - +
65F CYS* 4.1 1.3 - - + -
81F LEU* 3.9 24.9 - - + -
86F ILE* 4.3 2.0 - - + -
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Residues in contact with VAL 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ILE* 3.3 16.4 - - + +
25F PRO* 4.0 12.1 - - + -
31F VAL* 3.8 32.5 - - + +
34F ILE* 4.0 19.5 - - + -
35F ALA* 4.3 13.2 - - + -
38F MET* 3.7 30.1 - - + -
52F THR* 3.4 3.8 - - - +
53F TRP* 2.8 43.5 + - + +
55F ALA* 5.3 1.3 - - + -
62F VAL* 5.1 2.5 - - + +
63F ILE* 1.3 76.0 - - - +
65F CYS* 1.3 61.5 + - - +
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Residues in contact with CYS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU* 4.1 22.2 - - - -
23F ILE 3.0 8.1 + - - -
24F VAL* 3.3 29.4 - - + +
25F PRO* 3.9 4.0 - - - -
31F VAL* 4.9 0.2 - - - -
50F PHE* 5.0 0.7 - - - -
51F THR 3.5 5.4 - - - -
52F THR* 3.4 22.2 - - + +
63F ILE* 4.1 8.9 - - + +
64F VAL* 1.3 75.3 - - - +
66F SER* 1.3 75.1 + - - +
77F ALA* 4.6 3.8 - - - -
81F LEU* 3.7 32.3 - - + -
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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