Contacts of the helix formed by residues 14 - 28 (chain B) in PDB entry 4F4I
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 GLY 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY* 3.2 5.9 + - - +
13B SER* 1.3 77.5 - - - +
15B LYS* 1.3 63.5 + - - +
16B THR* 3.4 2.9 - - - -
17B THR* 3.2 7.0 + - - -
18B VAL* 3.0 28.0 + - - +
141B ARG* 4.1 4.6 - - - +
187B LEU* 4.4 24.5 - - - -
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.8 12.3 - - + -
8B GLU* 3.6 13.9 - - - +
9B GLY 3.1 41.5 - - - +
10B PRO 5.1 1.8 + - - +
13B SER* 3.3 13.9 + - - +
14B GLY* 1.3 75.5 - - - +
16B THR* 1.3 68.3 + - - +
18B VAL* 3.9 0.5 - - - +
19B ILE* 3.0 29.3 + - + +
91B ASP* 3.5 32.8 + - + +
92B ARG* 5.5 6.2 - - - +
131B LEU* 3.3 16.1 - - + +
167B TYR* 5.3 0.7 - - - -
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.4 0.6 - - - -
15B LYS* 1.3 86.0 + - - +
17B THR* 1.3 68.5 + - - +
19B ILE* 3.1 20.9 - - + +
20B ASN* 3.1 10.4 + - + +
36B ARG* 4.1 22.9 - - - +
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 3.2 7.5 + - - -
16B THR* 1.3 81.8 - - - +
18B VAL* 1.3 66.6 + - - +
20B ASN* 3.2 6.1 + - - +
21B GLU* 2.9 37.1 + - + +
187B LEU* 4.4 24.3 - - + +
191B VAL* 5.7 2.7 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 4.9 3.4 - - + -
14B GLY* 3.0 28.4 + - - +
15B LYS 3.9 2.2 - - - +
17B THR* 1.3 77.0 - - - +
19B ILE* 1.3 61.2 + - - +
21B GLU* 3.6 0.9 - - - +
22B VAL* 2.7 42.4 + - + +
131B LEU* 4.2 16.6 - - + -
187B LEU* 4.5 9.6 - - + +
190B VAL* 3.7 30.3 - - + +
191B VAL* 4.4 15.7 - - + -
194B THR* 3.8 25.6 - - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.5 47.8 - - + -
15B LYS* 3.0 21.8 + - + +
16B THR* 3.1 18.8 - - + +
18B VAL* 1.3 74.6 - - - +
20B ASN* 1.3 63.0 + - + +
22B VAL* 3.8 4.3 - - - +
23B TYR* 2.8 34.0 + - - +
34B MET* 3.5 45.1 - - + -
36B ARG* 6.1 1.6 - - - +
89B LEU* 4.2 4.9 - - + -
90B CYS 4.2 1.6 - - - -
91B ASP* 4.2 22.4 - - + +
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR* 3.1 10.7 + - + +
17B THR* 3.5 10.5 - - - +
19B ILE* 1.3 83.7 - - + +
21B GLU* 1.3 64.0 + - + +
23B TYR* 3.3 8.5 - - - +
24B HIS* 3.2 50.9 + - - -
34B MET* 4.7 8.8 - - - +
36B ARG* 3.5 26.9 + - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 2.9 29.5 + - + +
18B VAL 3.6 2.5 - - - +
20B ASN* 1.3 77.8 - - + +
22B VAL* 1.3 65.8 + - - +
24B HIS* 3.5 4.8 + - - +
25B ARG* 3.4 26.3 + - - +
191B VAL* 4.1 28.2 - - + +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 4.5 4.5 - - + -
18B VAL* 2.7 30.1 + - + +
19B ILE* 3.8 6.1 - - - +
21B GLU* 1.3 71.4 - - - +
23B TYR* 1.3 64.5 + - - +
25B ARG* 3.1 9.8 + - - +
26B LEU* 3.1 29.8 + - + +
89B LEU* 5.3 0.7 - - + -
191B VAL* 3.8 24.0 - - + +
194B THR* 3.6 26.0 - - + -
195B TYR* 4.2 12.1 - - + -
198B ILE* 3.4 31.9 - - + -
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Residues in contact with TYR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE 2.8 18.7 + - - +
20B ASN* 3.3 8.1 - - - +
22B VAL* 1.3 77.4 - - - +
24B HIS* 1.3 86.4 + + - +
26B LEU* 3.2 4.4 + - - +
27B VAL* 3.2 32.9 + - + +
32B VAL* 3.5 31.0 + - + -
33B ILE* 3.6 11.1 - - - +
34B MET* 3.5 54.5 + - + -
89B LEU* 4.1 14.1 - - + +
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Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASN* 3.2 40.3 + - - +
21B GLU* 3.5 5.3 + - - +
22B VAL 3.3 0.6 - - - -
23B TYR* 1.3 99.6 - + - +
25B ARG* 1.3 64.0 - - - +
27B VAL* 3.9 20.1 + - + +
28B LYS* 4.1 11.7 + - - +
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Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 3.4 13.6 + - - +
22B VAL* 3.1 8.0 + - - +
24B HIS* 1.3 79.3 - - - +
26B LEU* 1.3 63.3 + - - +
28B LYS* 3.2 45.6 - - + +
29B ASP* 5.2 0.5 - - - -
188B GLU* 5.0 2.8 + - - +
191B VAL* 3.8 26.7 - - - +
192B GLU* 2.8 34.5 + - - +
195B TYR* 3.4 45.9 + - + -
196B GLN* 5.3 0.4 - - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.1 23.9 + - + +
23B TYR 3.2 6.3 + - - +
25B ARG* 1.3 76.2 - - - +
27B VAL* 1.3 58.6 + - - +
29B ASP* 2.9 19.8 + - - -
30B TYR* 2.9 33.0 + - + -
32B VAL* 3.8 17.0 - - + -
87B VAL* 5.6 1.1 - - + -
89B LEU* 4.1 27.6 - - + -
195B TYR* 3.8 14.1 - - + -
198B ILE* 3.7 28.3 - - + -
199B ILE* 3.5 32.1 - - + -
202B LEU* 4.6 2.9 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 3.2 45.3 + - + +
24B HIS* 3.9 16.2 - - + +
25B ARG 3.3 0.2 - - - -
26B LEU* 1.3 74.3 - - - +
28B LYS* 1.3 69.2 + - - +
29B ASP 3.0 1.0 + - - -
30B TYR 3.5 11.6 + - - +
32B VAL* 3.7 16.8 - - + +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS 4.1 8.1 + - - +
25B ARG* 3.2 40.5 + - + +
27B VAL* 1.3 79.4 - - - +
29B ASP* 1.3 74.7 + - - +
195B TYR* 5.7 2.0 - - - +
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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
------------------------------------------------------------
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