Contacts of the helix formed by residues 24 - 36 (chain B) in PDB entry 1F3F
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 LEU 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B GLY* 3.0 14.8 + - - +
22B ARG* 3.9 46.9 - - + +
23B GLY* 1.3 82.1 - - - +
25B VAL* 1.3 65.7 + - - +
26B GLY 3.4 2.5 - - - -
27B GLU* 3.4 10.2 + - + +
28B ILE* 3.0 39.0 + - + +
112B PHE* 4.0 46.9 - - + -
120B ILE* 4.1 14.6 - - + -
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 4.2 9.4 - - + +
19B GLY 4.1 0.4 + - - -
20B VAL* 4.0 27.8 - - + +
23B GLY* 3.5 2.5 - - - -
24B LEU* 1.3 78.8 - - - +
26B GLY* 1.3 60.0 + - - +
28B ILE* 3.3 1.7 + - - +
29B ILE* 3.0 48.3 + - + +
42B LEU* 6.0 0.2 - - + -
78B VAL* 3.8 43.7 - - + -
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 5.2 1.4 + - - -
24B LEU 3.4 0.4 - - - -
25B VAL* 1.3 77.0 - - - +
27B GLU* 1.3 60.1 + - - +
29B ILE* 3.3 6.8 + - - +
30B ALA* 2.8 34.1 + - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 5.4 1.9 + - - +
24B LEU* 3.4 19.8 + - + +
25B VAL 3.3 0.2 - - - -
26B GLY* 1.3 75.1 - - - +
28B ILE* 1.3 64.8 + - + +
30B ALA* 3.4 7.4 + - - +
31B ARG* 2.7 59.4 + - - +
112B PHE* 3.5 33.3 - - + -
34C LYS* 6.5 0.2 - - - -
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 3.9 25.4 - - + -
24B LEU* 3.0 27.3 + - + +
25B VAL 3.7 3.6 - - - +
27B GLU* 1.3 78.6 - - + +
29B ILE* 1.3 68.2 + - - +
31B ARG* 3.0 16.5 + - - +
32B TYR* 3.3 25.0 + - + -
80B MET* 4.1 13.7 - - + -
108B ILE* 4.1 22.0 - - + -
112B PHE* 5.7 1.1 - - + -
120B ILE* 3.7 29.8 - - + -
121B ILE* 3.8 26.2 - - + -
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 5.6 0.2 - - + -
25B VAL* 3.0 36.6 + - + +
26B GLY* 3.8 5.4 - - - +
28B ILE* 1.3 76.5 - - - +
30B ALA* 1.3 57.5 + - - +
32B TYR* 3.1 5.3 + - - +
33B GLU* 2.8 49.5 + - + +
39B LEU* 4.8 10.1 - - + -
42B LEU* 4.1 32.1 - - + -
80B MET* 3.8 19.3 - - - -
82B PHE* 4.3 15.0 - - + -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY 2.8 19.0 + - - +
27B GLU* 3.6 9.6 - - - +
29B ILE* 1.3 78.4 - - - +
31B ARG* 1.3 56.7 + - + +
33B GLU* 3.6 14.5 + - - +
34B LYS* 2.8 53.6 + - - +
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Residues in contact with ARG 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASP 4.4 2.1 - - - +
27B GLU* 2.7 41.1 + - - +
28B ILE* 3.0 9.1 + - - +
30B ALA* 1.3 78.9 - - + +
32B TYR* 1.3 59.2 + - + +
34B LYS* 3.9 6.9 - - + +
35B LYS* 3.1 27.0 + - - +
94B MET* 3.5 17.4 + - + +
106B GLY 3.1 26.3 + - - -
107B SER 3.5 14.1 - - - -
108B ILE* 3.6 22.1 - - + +
111B ASP* 2.7 24.2 + - - -
112B PHE* 3.4 21.0 - - - -
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.5 26.9 - - + -
28B ILE* 3.3 29.1 + - + -
29B ILE 3.1 2.7 + - - +
31B ARG* 1.3 76.3 - - + +
33B GLU* 1.3 65.4 + - - +
35B LYS* 3.4 7.3 + - - +
36B GLY 3.4 0.2 + - - -
37B PHE* 3.2 38.3 + + + +
82B PHE* 3.5 32.1 - + + -
91B ALA* 3.0 44.9 + - + +
94B MET* 3.7 26.5 - - + +
95B ILE* 3.3 18.9 - - - +
108B ILE* 3.7 24.2 - - + +
121B ILE* 4.0 2.1 - - + +
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 5.0 0.9 + - - -
29B ILE* 2.8 37.1 + - + +
30B ALA* 3.6 15.6 - - - +
32B TYR* 1.3 77.5 - - - +
34B LYS* 1.3 63.8 + - + +
36B GLY* 3.0 15.6 + - - -
37B PHE 3.9 10.4 - - - +
39B LEU* 5.8 6.0 - - + +
82B PHE* 4.4 8.2 - - + -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 2.9 27.0 + - - +
111A ASP 3.7 3.4 - - - +
112A PHE* 3.6 35.4 - - + +
30B ALA* 2.8 39.6 + - - +
31B ARG* 3.9 6.5 - - + +
33B GLU* 1.3 74.6 - - + +
35B LYS* 1.3 57.9 + - - +
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO 3.1 22.0 + - - -
101A LEU* 4.3 2.7 + - - +
103A SER 4.8 1.8 + - - -
109A ARG 3.5 1.4 + - - -
110A GLY* 2.9 29.9 + - - +
111A ASP 3.2 11.2 + - - +
112A PHE* 3.1 15.6 - - - +
113A GLY 2.8 31.2 + - - +
114A VAL* 3.4 16.2 - - + +
31B ARG 3.1 17.8 + - - +
32B TYR 3.5 7.4 - - - +
33B GLU 3.2 0.4 - - - -
34B LYS* 1.3 76.8 - - - +
36B GLY* 1.3 57.8 + - - +
37B PHE* 3.3 25.6 - - + -
90B SER* 3.3 23.9 + - - -
93B LEU* 6.3 0.4 - - - +
94B MET* 3.8 15.4 - - + +
153B LEU* 4.0 0.7 - - - +
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 4.4 1.8 - - - -
114A VAL* 4.7 2.1 - - - +
33B GLU 3.0 12.2 + - - -
34B LYS 3.1 1.7 - - - -
35B LYS* 1.3 80.5 - - - +
37B PHE* 1.3 69.1 + - - +
38B VAL* 3.9 6.3 + - - +
83B GLU 4.7 0.3 - - - +
153B LEU* 2.9 41.1 - - - +
154B TYR* 4.5 8.8 + - - -
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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