Contacts of the helix formed by residues 29 - 42 (chain B) in PDB entry 4L2A
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 LYS 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.4 36.4 + - + +
24B GLU 3.6 6.7 + - - +
25B PHE* 2.8 41.2 + - + +
28B GLY* 1.3 81.6 - - - +
30B HIS* 1.3 60.4 + - - +
32B ASN* 3.7 2.4 - - - +
33B THR* 2.7 39.1 + - - +
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Residues in contact with HIS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 3.6 10.8 - - - -
163A TYR* 6.5 0.2 - + - -
164A TYR* 2.6 35.1 + + - -
169A ASN* 3.5 26.6 - - + +
25B PHE 2.8 26.2 + - - -
26B HIS* 3.2 23.3 - - + +
29B LYS* 1.3 77.5 - - - +
31B HIS* 1.3 64.4 + - - +
33B THR* 3.1 10.7 + - - -
34B TYR* 3.3 26.6 + - + -
161B HIS* 3.4 39.2 + + + +
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.5 14.2 - - + +
5B PRO* 4.1 14.7 - - + +
26B HIS* 2.9 16.4 + - - +
27B HIS* 3.2 18.0 + - - +
29B LYS 3.5 0.2 - - - -
30B HIS* 1.3 70.1 - - - +
32B ASN* 1.3 64.7 + - - +
34B TYR* 3.0 21.3 + + - +
35B VAL* 3.2 9.7 + - + +
69B GLN 4.6 0.2 - - - -
70B ILE* 3.2 36.5 + - + +
73B HIS* 3.5 17.4 - + + +
74B THR* 3.2 30.3 + - - -
77B TRP* 2.8 33.6 + + - +
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Residues in contact with ASN 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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4B LEU* 3.8 30.0 - - + +
27B HIS 3.3 4.2 + - - +
28B GLY 3.2 27.7 + - - +
29B LYS* 3.7 3.4 + - - +
31B HIS* 1.3 79.0 - - - +
33B THR* 1.3 64.4 + - - +
35B VAL* 2.9 9.8 + - - +
36B VAL* 2.9 36.6 + - - +
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASN* 5.2 4.9 + - - -
29B LYS* 2.7 29.5 + - - +
30B HIS* 3.1 6.7 + - - -
32B ASN* 1.3 75.3 + - - +
34B TYR* 1.3 64.6 + - + +
36B VAL* 3.3 10.7 + - + +
37B LYS* 2.8 56.8 + - + +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 4.1 15.2 - + - -
30B HIS* 3.3 30.0 + - + -
31B HIS* 3.0 9.2 + - - +
33B THR* 1.3 81.4 - - + +
35B VAL* 1.3 58.2 + - - +
38B LEU* 2.9 31.0 + - - +
66B ASN* 3.3 28.9 - - - +
69B GLN* 3.2 45.1 + - + -
70B ILE* 3.7 19.4 - - + +
73B HIS* 3.5 29.6 - + - -
159B TRP* 3.6 21.3 - - - -
161B HIS* 4.4 5.1 - + - -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PHE* 3.4 37.2 - - + +
3B GLU* 3.9 10.1 - - - +
4B LEU* 4.1 21.8 - - + +
31B HIS* 3.6 18.8 - - + +
32B ASN* 2.9 12.1 + - - +
34B TYR* 1.3 78.7 - - - +
36B VAL* 1.3 64.0 + - + +
38B LEU* 3.9 1.4 - - - +
39B ASN* 3.1 26.2 + - - +
70B ILE* 3.8 30.2 - - + +
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Residues in contact with VAL 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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32B ASN* 2.9 31.8 + - - +
33B THR* 3.3 17.3 - - + +
35B VAL* 1.3 78.3 - - + +
37B LYS* 1.3 74.1 + - + +
39B ASN* 3.7 8.0 - - - +
40B GLY* 3.1 19.1 + - - -
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 4.5 18.8 - - - +
33B THR* 2.8 40.0 + - + +
36B VAL* 1.3 79.5 - - + +
38B LEU* 1.3 64.2 + - - +
40B GLY* 3.1 4.3 + - - -
41B LEU* 3.0 25.9 + - + +
66B ASN* 3.3 36.3 - - - +
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Residues in contact with LEU 38 (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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2B PHE* 3.5 32.8 - - + -
34B TYR 2.9 19.4 + - - +
35B VAL 4.0 2.7 - - - +
37B LYS* 1.3 76.5 - - - +
39B ASN* 1.3 58.9 + - - +
41B LEU* 2.8 20.5 + - + +
42B ILE* 3.1 40.0 + - + +
52B LEU* 4.2 4.0 - - + -
55B ILE* 4.6 2.9 - - + -
63B VAL* 3.7 36.1 - - + +
66B ASN* 4.1 9.5 - - + +
67B ALA* 4.0 16.2 - - + +
70B ILE* 3.6 19.7 - - + -
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Residues in contact with ASN 39 (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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1B ALA* 3.5 18.9 - - + +
2B PHE* 2.7 61.2 - - - +
35B VAL* 3.1 20.6 + - - +
36B VAL* 3.7 7.7 - - - +
37B LYS 3.3 0.2 - - - -
38B LEU* 1.3 77.6 - - - +
40B GLY* 1.3 57.8 - - - +
42B ILE* 4.0 6.7 - - - +
43B PRO* 2.9 27.4 - - - +
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Residues in contact with GLY 40 (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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36B VAL 3.1 12.8 + - - -
37B LYS 3.5 4.5 - - - -
38B LEU 3.0 0.6 - - - -
39B ASN* 1.3 79.2 - - - +
41B LEU* 1.3 60.2 + - - +
43B PRO* 3.7 12.0 - - - +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 3.0 14.7 + - + +
38B LEU* 2.8 12.6 + - + +
40B GLY* 1.3 81.6 - - - +
42B ILE* 1.3 64.1 + - + +
43B PRO 3.5 5.6 - - - +
45B THR* 4.3 9.2 + - - +
62B GLY* 3.7 35.7 - - - +
63B VAL* 3.7 22.8 - - + +
66B ASN* 4.0 11.7 - - - +
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Residues in contact with ILE 42 (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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1B ALA* 5.8 2.5 - - - -
2B PHE* 3.8 33.2 - - + -
38B LEU* 3.5 34.8 - - + +
39B ASN* 4.0 8.7 - - - +
41B LEU* 1.3 73.4 - - - +
43B PRO* 1.3 83.5 - - + +
44B GLY 3.2 0.3 + - - -
45B THR* 2.5 26.8 + - - -
47B PHE* 4.0 24.7 - - + +
48B GLU* 4.0 26.6 + - + +
55B ILE* 4.5 5.4 - - + -
63B VAL* 4.5 7.0 - - + -
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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
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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