Contacts of the strand formed by residues 108 - 114 (chain A) in PDB entry 1FIK
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 THR 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TRP* 5.3 2.0 - - + -
21A ILE* 3.8 14.4 - - + -
22A VAL 3.2 11.0 - - - +
23A GLY* 4.3 0.2 - - - -
24A TYR* 3.4 11.1 - - - -
31A TRP* 3.4 38.8 - - + -
103A THR 3.8 0.2 - - - +
104A LYS* 3.4 2.9 - - - -
105A THR* 2.7 57.1 + - - +
107A LYS* 1.3 79.7 - - - +
109A LEU* 1.3 64.8 + - - +
110A VAL* 4.1 2.1 - - - +
134A LEU* 4.1 11.1 - - + +
139A TYR 3.5 9.1 + - - +
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Residues in contact with LEU 109 (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 ALA 3.8 0.9 - - - +
21A ILE* 3.7 2.3 - - - -
22A VAL* 2.7 43.4 + - + +
24A TYR* 3.7 17.9 - - + -
47A VAL* 3.9 31.4 - - + -
50A LEU* 3.9 21.1 - - + -
51A VAL* 3.8 20.4 - - + -
77A LEU* 4.7 4.9 - - + -
102A VAL* 4.1 15.9 - - + -
103A THR 3.4 3.4 - - - +
104A LYS* 3.8 18.2 - - + +
108A THR* 1.3 80.9 - - - +
110A VAL* 1.3 60.9 + - - +
111A LEU* 3.9 7.8 - - + +
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Residues in contact with VAL 110 (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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10A LEU* 4.2 25.1 - - + -
20A ALA 3.7 7.0 - - - +
21A ILE* 4.6 7.6 - - + -
102A VAL* 3.4 1.7 - - - -
103A THR* 2.7 43.7 + - - +
105A THR* 4.4 1.1 - - + -
108A THR* 4.2 6.1 - - - +
109A LEU* 1.3 74.6 - - - +
111A LEU* 1.3 60.4 + - - +
127A CYS* 3.2 20.7 - - - +
130A MET* 4.3 13.9 - - + -
131A ALA* 4.2 14.6 - - + -
134A LEU* 3.5 30.3 - - + -
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Residues in contact with LEU 111 (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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10A LEU* 5.1 0.3 - - - +
19A ALA* 3.2 6.1 - - - +
20A ALA* 3.1 35.2 + - + +
22A VAL* 3.6 30.5 - - + -
39A PHE* 3.6 20.2 - - + -
42A ILE* 3.6 25.1 - - + -
50A LEU* 4.7 4.5 - - + -
65A LEU* 4.0 20.2 - - + -
101A THR 3.4 4.9 - - - +
102A VAL* 3.8 28.0 - - + -
109A LEU* 3.9 14.4 - - + +
110A VAL* 1.3 78.8 - - - +
112A LEU* 1.3 63.3 + - - +
127A CYS* 4.4 0.7 - - - -
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Residues in contact with LEU 112 (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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10A LEU* 4.0 24.0 - - + +
16A CYS* 3.6 33.4 - - + -
18A ASP 3.6 13.0 - - - +
19A ALA* 4.1 10.8 - - + -
39A PHE* 3.8 4.6 - - - -
100A VAL* 3.2 6.2 - - - +
101A THR 2.9 33.9 + - - +
111A LEU* 1.3 76.5 - - - +
113A MET* 1.3 59.4 + - - +
123A ILE* 3.3 36.9 - - + +
126A LYS* 3.8 22.0 - - + -
127A CYS* 4.0 15.0 - - + +
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Residues in contact with MET 113 (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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16A CYS* 3.4 7.7 - - - +
17A GLN* 2.9 56.5 + - + +
18A ASP* 2.7 27.3 + - + +
38A THR* 3.7 29.6 - - + +
39A PHE* 3.8 20.4 - - + -
68A GLN* 5.1 6.3 - - + +
70A CYS* 6.4 0.4 - - - -
89A THR* 4.0 18.8 - - + -
98A PHE* 3.9 17.7 - - + -
99A ASN 3.5 1.8 - - - -
100A VAL* 4.0 9.4 - - + +
112A LEU* 1.3 73.0 - - - +
114A GLY* 1.3 64.1 + - - +
123A ILE* 4.4 2.7 - - - -
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Residues in contact with GLY 114 (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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15A THR 3.8 3.6 - - - -
17A GLN* 2.9 20.3 + - - -
98A PHE* 3.4 11.4 - - - +
99A ASN* 2.8 18.7 + - - -
113A MET* 1.3 74.4 - - - +
115A LYS* 1.3 67.5 + - - +
118A VAL* 4.8 2.0 - - - -
123A ILE* 3.4 27.8 - - - +
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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