Contacts of the helix formed by residues 14 - 32 (chain B) in PDB entry 2FIU
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 ASP 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.6 2.0 - - - -
13B ARG* 1.3 80.6 - - - +
15B SER* 1.3 58.9 + - - +
16B GLU* 3.5 10.7 + - - +
17B ARG* 3.3 39.2 + - - +
18B TYR* 3.0 26.2 + - - +
84B VAL* 3.2 23.3 + - + +
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.7 18.1 - - - +
14B ASP* 1.3 70.6 + - - +
16B GLU* 1.3 66.2 + - - +
18B TYR* 3.7 2.3 - - - +
19B LYS* 3.4 18.2 + - - +
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 3.3 8.5 + - - +
15B SER* 1.3 80.4 + - - +
17B ARG* 1.3 64.7 + - + +
19B LYS* 2.5 56.7 + - - +
20B ASP* 3.7 1.0 + - - +
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 3.3 25.8 + - - +
16B GLU* 1.3 86.0 - - + +
18B TYR* 1.3 59.9 + - - +
19B LYS 3.3 0.2 - - - -
20B ASP* 3.1 35.8 + - - +
21B TYR 3.4 4.5 + - - -
80B ILE* 3.4 24.6 + - + +
83B GLU* 3.3 29.5 + - - +
84B VAL* 3.6 34.2 - - + +
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Residues in contact with TYR 18 (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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10B VAL* 3.6 40.6 - - + +
12B VAL* 3.5 36.1 - - + -
14B ASP 3.0 8.0 + - - +
15B SER* 3.8 6.1 - - - +
16B GLU 3.2 0.6 - - - -
17B ARG* 1.3 72.5 - - - +
19B LYS* 1.3 61.9 + - - +
20B ASP 3.1 1.3 - - - -
21B TYR* 3.1 33.9 + + - +
22B VAL* 3.0 42.2 + - + +
39B ARG* 5.0 6.2 + - - -
53B ARG* 4.0 22.6 - - - +
55B VAL* 5.6 2.1 - - - +
81B ARG* 3.9 13.8 - - + -
84B VAL* 4.0 10.3 - - + -
85B ALA* 4.0 9.2 - - + -
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER 3.4 7.1 + - - +
16B GLU* 2.5 57.0 + - - +
18B TYR* 1.3 80.3 - - - +
20B ASP* 1.3 84.1 + - - +
22B VAL* 3.8 9.3 - - - +
23B SER* 2.9 33.0 + - - -
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 5.1 0.6 - - - +
17B ARG* 3.1 32.1 + - - +
18B TYR 3.1 0.6 - - - -
19B LYS* 1.3 106.1 + - - +
21B TYR* 1.3 57.1 + - - +
23B SER* 3.4 5.6 + - - -
24B THR* 2.9 33.9 + - + +
80B ILE* 4.1 16.6 - - + +
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TRP* 5.5 0.2 + - - -
17B ARG 3.4 2.4 + - - +
18B TYR* 3.1 48.6 + + - +
20B ASP* 1.3 76.4 - - - +
22B VAL* 1.3 69.2 + - + +
24B THR* 3.3 4.7 + - - -
25B ALA* 2.9 42.5 + - + +
29B PHE* 4.4 6.8 - - - -
39B ARG* 4.5 9.4 + - - -
74B TYR* 2.6 45.7 + + - -
77B ALA* 3.2 31.0 - - + +
78B ALA 4.3 0.4 - - - -
80B ILE* 4.1 14.7 - - + +
81B ARG* 3.2 31.3 + - + +
89B MSE 4.5 3.8 - - - +
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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
----------------------------------------------------------
18B TYR* 3.0 40.1 + - + +
19B LYS* 3.2 10.3 + - - +
21B TYR* 1.3 81.2 - - + +
23B SER* 1.3 63.4 + - - +
25B ALA* 3.6 3.1 + - - +
26B LYS* 3.3 22.2 + - + +
29B PHE* 5.5 1.0 - - - -
39B ARG* 3.3 36.7 + - - +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS 2.9 17.6 + - - -
20B ASP* 3.4 10.0 + - - -
22B VAL* 1.3 80.9 - - - +
24B THR* 1.3 63.8 + - - +
25B ALA 3.4 0.2 - - - -
26B LYS* 3.6 10.5 - - - +
27B PRO* 3.4 16.3 - - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 2.9 23.4 + - + +
21B TYR* 3.5 1.2 + - - -
23B SER* 1.3 78.9 - - - +
25B ALA* 1.3 62.7 + - - +
26B LYS 3.3 0.7 - - - -
27B PRO* 3.6 13.6 - - - +
73B GLU* 4.4 14.3 - - - +
77B ALA* 3.4 27.5 - - - +
80B ILE* 4.0 9.3 - - + +
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Residues in contact with ALA 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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21B TYR* 2.9 25.3 + - + +
22B VAL* 4.0 3.6 - - - +
23B SER 3.4 0.2 - - - -
24B THR* 1.3 76.8 + - - +
26B LYS* 1.3 65.4 + - - +
27B PRO 3.4 0.2 - - - -
28B ALA* 2.9 18.7 + - - +
29B PHE* 3.2 34.8 + - + -
74B TYR* 3.8 22.2 - - + +
77B ALA* 3.8 9.2 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL* 3.3 12.6 + - + +
23B SER* 3.6 11.9 - - - +
25B ALA* 1.3 78.0 - - - +
27B PRO* 1.3 69.9 - - + +
29B PHE* 3.2 13.0 + - + +
30B GLU* 2.9 54.7 + - + +
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Residues in contact with PRO 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER 3.4 12.8 - - - +
24B THR* 3.6 11.0 - - - +
25B ALA 3.5 3.8 - - - -
26B LYS* 1.3 97.4 - - + +
28B ALA* 1.3 55.1 + - - +
30B GLU* 4.0 7.0 - - + +
31B ARG* 3.1 29.9 + - - +
73B GLU* 5.3 11.2 - - + -
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Residues in contact with ALA 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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25B ALA 2.9 15.1 + - - +
27B PRO* 1.3 70.9 - - - +
29B PHE* 1.3 66.1 + - - +
31B ARG* 3.2 7.5 + - - +
32B PHE* 3.1 31.9 + - + -
68B CYS* 3.7 9.2 - - - -
71B SER* 3.6 24.9 - - - +
73B GLU* 4.2 9.6 - - + +
74B TYR* 3.8 24.7 - - + +
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Residues in contact with PHE 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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6B TRP* 3.6 32.5 - + - -
21B TYR* 4.4 6.5 - - - -
22B VAL 5.5 0.7 - - - -
25B ALA* 3.2 35.9 + - + -
26B LYS* 3.7 9.4 - - + +
28B ALA* 1.3 77.8 - - - +
30B GLU* 1.3 63.0 + - + +
32B PHE* 3.4 1.4 + - - +
33B GLY 3.4 3.3 + - - -
34B ALA* 3.0 39.7 + - + -
36B PHE* 3.8 25.4 - + + -
39B ARG* 4.8 13.0 - - - -
57B ILE* 3.7 18.8 - - + -
59B PHE* 4.0 9.9 - + - -
68B CYS* 3.7 16.2 - - - -
74B TYR* 3.6 20.0 - + - -
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Residues in contact with GLU 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 LYS* 2.9 51.1 + - + +
27B PRO* 4.1 6.3 - - + +
29B PHE* 1.3 79.6 - - + +
31B ARG* 1.3 63.2 + - - +
32B PHE 3.2 0.5 + - - -
33B GLY* 3.3 11.7 + - - -
34B ALA 5.0 2.9 - - - +
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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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27B PRO 3.1 19.4 + - - +
28B ALA* 3.2 7.1 + - - +
30B GLU* 1.3 75.9 - - - +
32B PHE* 1.3 96.8 + - + +
33B GLY 3.8 0.9 + - - -
71B SER* 3.9 5.3 - - - -
72B PRO* 4.5 4.9 - - - +
73B GLU* 3.1 31.7 + - - -
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Residues in contact with PHE 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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28B ALA* 3.1 25.8 + - - +
29B PHE 3.4 0.2 + - - -
30B GLU 3.2 0.4 - - - -
31B ARG* 1.3 126.1 - - + +
33B GLY* 1.3 60.8 + - - +
34B ALA 3.5 1.8 - - - -
59B PHE* 3.5 14.6 - - + -
60B PRO* 3.6 2.1 - - - +
64B HIS* 3.5 43.7 + - - +
67B ASP* 3.5 32.1 - - + -
68B CYS* 3.6 26.7 - - + -
71B SER* 3.9 14.6 - - - -
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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