Contacts of the helix formed by residues 40 - 59 (chain B) in PDB entry 3IAB
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 PRO 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR 3.4 4.3 - - - +
39B THR* 1.3 93.2 - - - +
41B TYR* 1.3 65.7 + - - +
42B VAL 3.5 0.4 - - - +
43B SER* 3.8 4.9 - - - +
44B ALA* 3.2 16.6 + - - +
74B LYS* 5.0 0.4 - - - -
68R A 3.9 11.2 - - - +
69R A 3.5 22.7 - - - +
70R U 5.9 1.3 - - + -
73R G 3.5 20.6 - - + +
88R C 3.5 35.7 - - - +
89R U 3.7 7.9 - - - +
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 4.5 1.0 - - - +
39B THR 4.0 0.4 + - - -
40B PRO* 1.3 73.6 - - - +
42B VAL* 1.3 60.4 + - + +
44B ALA* 3.2 9.3 + - - +
45B LEU* 3.0 46.6 + - + +
74B LYS* 4.7 4.9 - - + -
77B ALA* 3.6 9.1 + - + -
78B LEU* 3.6 37.1 - - + +
81B HIS* 3.3 32.3 - + - +
68R A 3.8 35.2 + + + +
71R A 3.3 69.5 - + + +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 3.5 1.2 - - - +
41B TYR* 1.3 75.1 - - + +
43B SER* 1.3 61.3 + - - +
45B LEU* 4.1 9.2 - - + -
46B LYS* 2.8 34.4 + - - +
71R A 3.6 31.4 - - - +
72R U 3.2 48.2 - - + +
73R G 3.4 43.1 - - + +
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 3.5 19.2 + - - -
42B VAL* 1.3 78.0 - - - +
44B ALA* 1.3 57.6 + - - +
46B LYS* 3.7 2.7 + - - +
47B ARG* 3.2 31.9 + - - +
73R G 4.1 4.2 - - - +
88R C 3.4 49.9 + - - +
89R U 2.8 26.0 + - - -
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 6.3 2.5 - - + -
35B VAL* 5.2 6.3 - - + -
39B THR* 3.8 16.5 - - + +
40B PRO 3.2 9.3 + - - +
41B TYR* 3.2 11.3 + - - +
42B VAL 3.1 0.6 - - - -
43B SER* 1.3 78.2 - - - +
45B LEU* 1.3 64.2 + - - +
47B ARG* 3.4 6.1 + - - +
48B ILE* 3.0 33.2 + - + +
74B LYS* 6.1 0.9 - - + -
78B LEU* 3.8 26.5 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 3.0 40.7 + - + +
42B VAL* 3.4 12.8 - - + +
44B ALA* 1.3 76.3 - - - +
46B LYS* 1.3 64.3 + - - +
48B ILE* 3.1 4.2 + - - +
49B ASN* 2.9 29.2 + - - +
78B LEU* 3.8 15.3 - - + -
81B HIS* 3.4 40.2 - - + +
82B PHE* 3.6 16.7 - - + -
72R U 3.7 37.9 - - + +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 2.8 20.6 + - - +
43B SER* 3.9 4.9 - - - +
45B LEU* 1.3 73.4 - - - +
47B ARG* 1.3 63.2 + - - +
49B ASN* 3.4 8.7 + - - +
50B LYS* 3.1 44.2 + - - +
72R U 3.1 34.9 + - + +
73R G 2.9 43.3 + - - +
74R C 4.2 6.9 - - - +
87R G 4.6 2.0 + - - -
88R C 4.0 11.0 - - - +
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Residues in contact with ARG 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.7 22.2 - - + -
39B THR* 6.0 1.0 - - - +
43B SER* 3.2 22.3 + - - +
44B ALA* 3.8 7.0 - - - +
45B LEU 3.2 0.4 - - - -
46B LYS* 1.3 79.6 - - - +
48B ILE* 1.3 62.0 + - - +
50B LYS* 3.5 7.2 + - + +
51B PHE* 3.1 40.0 + - + -
88R C 3.5 35.6 + - - -
89R U 2.6 76.2 + - - +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.5 24.2 - - + -
35B VAL* 5.9 0.4 - - + -
44B ALA* 3.0 22.6 + - + +
47B ARG* 1.3 71.9 - - - +
49B ASN* 1.3 65.3 + - - +
51B PHE* 3.0 4.5 + - - +
52B LEU* 2.8 27.7 + - + +
63B VAL* 4.4 11.7 - - + -
65B VAL* 4.1 18.8 - - + -
78B LEU* 4.3 24.2 - - + -
82B PHE* 3.5 36.6 - - + -
138B ILE* 3.9 20.4 - - + -
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Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 2.9 20.1 + - - +
46B LYS* 3.5 10.3 - - - +
48B ILE* 1.3 74.7 - - - +
50B LYS* 1.3 67.7 + - + +
52B LEU* 3.0 23.5 + - - +
53B ASP* 3.2 21.2 + - - +
82B PHE* 3.4 15.2 - - - -
86B LYS* 3.0 22.8 + - - +
72R U 2.7 32.3 + - - +
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Residues in contact with LYS 50 (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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46B LYS* 3.1 33.4 + - - +
47B ARG* 3.7 8.7 - - + +
48B ILE 3.3 0.4 - - - -
49B ASN* 1.3 80.3 - - - +
51B PHE* 1.3 61.5 + - + +
53B ASP* 3.5 12.0 + - - +
54B SER* 3.1 29.0 + - - -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE 4.7 0.7 - - - -
30B HIS* 3.2 40.8 - - - +
31B THR* 3.9 11.7 - - - -
32B THR 3.8 13.2 - - - -
33B ILE* 3.6 18.8 - - + -
47B ARG* 3.1 36.4 + - + +
48B ILE 3.0 9.3 + - - +
50B LYS* 1.3 77.5 - - + +
52B LEU* 1.3 60.6 + - - +
54B SER* 3.8 6.2 - - - -
55B VAL* 2.9 32.4 + - - +
63B VAL* 3.5 17.6 - - + +
89R U 3.4 30.1 - + - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 2.8 18.7 + - + +
49B ASN* 3.0 15.4 + - - +
51B PHE* 1.3 77.0 - - - +
53B ASP* 1.3 65.0 + - - +
55B VAL* 3.2 19.0 - - - +
56B HIS* 3.4 12.1 + - - -
63B VAL* 3.8 20.2 - - + -
82B PHE* 3.4 35.4 - - + -
86B LYS* 6.0 0.4 - - + -
88B LYS* 4.6 16.4 - - + +
138B ILE* 4.0 27.6 - - + +
139B TYR 4.8 0.4 - - - +
140B VAL* 3.7 21.2 - - + +
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Residues in contact with ASP 53 (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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49B ASN* 3.2 20.0 + - - +
50B LYS* 3.9 12.6 - - - +
52B LEU* 1.3 82.3 - - - +
54B SER* 1.3 60.1 + - - +
56B HIS* 3.0 29.0 + - - +
57B LYS* 4.6 8.0 + - - -
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Residues in contact with SER 54 (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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30B HIS* 5.3 5.5 + - - +
50B LYS 3.1 17.9 + - - -
51B PHE* 3.8 7.0 - - - -
52B LEU 3.4 0.2 - - - -
53B ASP* 1.3 73.4 - - - +
55B VAL* 1.3 60.9 + - - +
56B HIS 3.1 5.4 - - - -
57B LYS* 3.2 33.0 + - - +
58B GLN* 3.4 20.5 + - - +
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Residues in contact with VAL 55 (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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30B HIS 5.4 1.3 - - - +
31B THR* 3.7 24.9 - - + -
51B PHE 2.9 15.4 + - - +
52B LEU* 3.2 12.6 - - - +
54B SER* 1.3 74.8 - - - +
56B HIS* 1.3 60.6 + - - +
57B LYS 3.3 0.2 - - - -
58B GLN* 3.7 5.8 - - - -
59B GLY* 3.0 23.9 + - - -
60B SER* 3.3 26.0 + - - +
61B SER 4.9 0.7 - - - +
62B TYR 3.7 21.1 - - - +
63B VAL* 4.2 6.3 - - + -
140B VAL* 3.1 35.2 - - + -
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Residues in contact with HIS 56 (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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52B LEU 3.4 19.5 + - - -
53B ASP* 3.0 29.7 + - - +
54B SER 3.1 0.2 - - - -
55B VAL* 1.3 81.5 - - - +
57B LYS* 1.3 63.4 - - + +
59B GLY* 3.5 8.8 + - - -
60B SER 5.4 0.4 - - - -
140B VAL* 4.3 24.3 - - + +
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASP 4.6 6.8 + - - +
54B SER* 3.2 28.4 + - - +
56B HIS* 1.3 78.7 - - + +
58B GLN* 1.3 66.0 + - + +
59B GLY* 3.5 0.9 + - - -
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Residues in contact with GLN 58 (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 HIS* 5.3 4.5 + - - -
27B LYS* 4.1 35.8 - - + +
30B HIS* 3.5 52.8 + - + +
31B THR* 4.1 16.8 - - + -
54B SER* 3.4 19.4 + - - +
55B VAL* 3.9 7.6 - - - +
56B HIS 3.3 0.6 - - - -
57B LYS* 1.3 80.8 - - + +
59B GLY* 1.3 61.4 + - - +
60B SER* 5.2 0.4 - - - -
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Residues in contact with GLY 59 (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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55B VAL 3.0 6.3 + - - -
56B HIS 3.5 7.1 + - - -
57B LYS 3.3 3.8 - - - -
58B GLN* 1.3 79.2 - - - +
60B SER* 1.3 60.9 + - - +
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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
------------------------------------------------------------
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