Contacts of the strand formed by residues 11 - 17 (chain A) in PDB entry 1F89
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 ILE 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.7 18.4 - - + -
9A GLN* 3.7 10.3 - - + +
10A LYS* 1.3 77.5 - - - +
12A LYS* 1.3 62.4 + - - +
13A VAL* 4.6 6.1 - - + -
47A LYS* 4.1 17.7 - - + +
48A LEU* 4.9 10.3 - - + -
161A TYR* 3.5 46.7 - - + -
187A PHE* 4.0 11.4 - - + -
261A GLU* 4.2 0.7 - - - -
262A LEU* 2.9 60.7 + - + +
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Residues in contact with LYS 12 (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 LYS 4.2 1.1 + - - +
11A ILE* 1.3 74.7 - - - +
13A VAL* 1.3 62.4 + - - +
43A GLN* 3.3 28.2 - - - +
45A ASP* 2.9 51.2 + - + +
46A THR* 3.7 0.9 - - - -
47A LYS* 3.0 31.1 + - - +
48A LEU 3.7 1.2 + - - -
260A ALA 3.2 9.6 - - - +
261A GLU* 3.6 35.7 - - + +
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Residues in contact with VAL 13 (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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11A ILE* 4.0 4.9 - - + +
12A LYS* 1.3 79.1 - - - +
14A ALA* 1.3 63.6 + - - +
15A LEU* 5.5 2.0 - - + +
43A GLN* 3.2 13.8 + - - -
46A THR* 4.4 0.7 - - - -
48A LEU* 3.3 28.9 - - + +
50A VAL* 6.2 0.4 - - + -
220A MET* 4.1 27.1 - - + -
240A VAL* 4.7 6.5 - - + -
259A TYR* 3.4 2.9 - - - -
260A ALA* 2.9 49.1 + - + +
262A LEU* 4.0 28.7 - - + -
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Residues in contact with ALA 14 (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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13A VAL* 1.3 76.8 - - - +
15A LEU* 1.3 66.0 - - - +
16A VAL* 3.9 0.6 + - + -
39A ALA* 4.2 17.3 - - + -
46A THR* 4.4 13.7 - - + +
48A LEU 3.0 7.9 + - - +
49A VAL* 3.4 8.9 - - + +
50A VAL* 3.0 25.3 + - - +
257A ILE* 4.2 3.1 - - + -
258A ILE 3.4 5.8 - - - +
259A TYR* 3.8 24.9 - - + -
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Residues in contact with LEU 15 (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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13A VAL* 5.5 2.2 - - + +
14A ALA* 1.3 75.0 - - - +
16A VAL* 1.3 60.4 + - - +
17A GLN 3.7 1.5 + - - -
50A VAL* 3.4 37.5 - - + -
220A MET* 4.1 18.4 - - + -
221A LEU 3.5 19.1 - - - +
222A CYS* 4.3 7.9 - - + -
238A SER* 4.5 6.7 - - - -
239A ILE 3.4 25.6 - - - +
240A VAL* 3.7 19.3 - - + -
257A ILE* 3.4 5.7 - - - +
258A ILE* 3.1 49.7 + - + +
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Residues in contact with VAL 16 (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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14A ALA 4.5 1.3 - - - +
15A LEU* 1.3 75.6 - - - +
17A GLN* 1.3 51.9 + - - +
18A LEU* 2.8 28.7 + - + +
32A ALA 5.6 0.2 - - - +
35A PHE* 3.8 37.2 - - + +
36A ILE* 4.4 8.3 - - + -
39A ALA* 4.8 4.0 - - + -
49A VAL* 4.2 15.5 - - + -
50A VAL 2.9 20.6 + - - +
51A LEU* 3.7 20.2 - - + -
52A PRO* 3.1 21.1 - - - +
222A CYS* 3.6 5.3 - - - -
256A GLU 4.0 1.8 - - - -
257A ILE* 4.4 13.9 - - + +
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Residues in contact with GLN 17 (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 LEU 3.7 2.8 + - - +
16A VAL* 1.3 67.7 - - - +
18A LEU* 1.3 61.0 + - - +
35A PHE* 6.1 0.2 - - - -
222A CYS* 4.6 0.2 - - - -
223A SER 3.1 20.0 - - - +
224A PRO 3.8 9.9 - - - +
225A ALA* 3.8 0.6 - - - +
236A GLY* 3.5 10.3 - - - -
237A HIS 3.3 2.8 + - - +
238A SER* 2.5 45.4 + - - +
251A ALA* 3.5 10.9 - - + +
252A GLY 2.8 27.5 + - - -
253A GLU 3.6 5.9 + - - -
254A GLY 2.9 21.6 + - - +
255A GLU* 3.3 8.1 - - - +
256A GLU* 2.8 40.2 + - + +
258A ILE* 6.4 0.7 - - + -
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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