Contacts of the helix formed by residues 25 - 37 (chain X) in PDB entry 4LAH
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 25 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X TRP* 3.9 16.7 + - + -
24X HIS* 1.3 78.5 + - - +
26X PRO* 1.4 68.4 - - - +
27X ASN 3.2 2.0 - - - -
28X ASP* 3.0 27.3 + - + +
29X LEU* 3.0 19.8 - - - +
112X THR* 4.6 0.7 - - + -
114X ILE* 3.7 25.1 - - + -
146X ASN* 3.4 35.4 - - + +
147X THR 4.5 0.2 - - - +
148X ILE* 3.9 20.2 - - + +
150X HIS* 3.6 40.6 - - + +
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Residues in contact with PRO 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X HIS* 3.5 26.7 - - + +
25X LEU* 1.4 84.5 - - - +
27X ASN* 1.3 60.9 + - - +
29X LEU* 3.0 15.4 + - + +
30X LYS* 3.0 43.0 + - - +
145X LYS* 3.3 47.3 - - + +
146X ASN* 3.3 9.2 - - - +
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Residues in contact with ASN 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X LEU* 4.8 0.4 - - + -
26X PRO* 1.3 72.2 - - - +
28X ASP* 1.3 57.8 + - - +
30X LYS* 2.8 30.2 + - - +
31X HIS* 2.9 28.8 + - - +
141X LYS* 3.5 25.3 + - - +
143X ASP* 4.8 4.7 + - - +
146X ASN* 2.7 37.0 + - - +
150X HIS* 4.0 18.2 + - - +
152X PHE* 4.2 7.8 - - + -
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Residues in contact with ASP 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ALA* 4.0 11.5 - - - +
21X LEU* 5.0 3.8 - - - +
23X TRP* 5.1 3.3 + - + +
25X LEU* 3.0 32.7 + - + +
27X ASN* 1.3 76.8 - - - +
29X LEU* 1.3 66.2 + - + +
31X HIS* 3.3 7.3 + - - +
32X VAL* 3.0 26.9 + - - +
112X THR* 2.8 30.1 + - + -
114X ILE* 5.4 0.4 - - + -
152X PHE* 4.5 4.5 - - - -
201X 1VO 2.8 39.5 + - - -
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Residues in contact with LEU 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X LEU* 4.2 13.2 - - + -
23X TRP* 6.6 0.2 - - + -
24X HIS* 6.2 1.6 - - + +
25X LEU 3.0 38.4 - - - +
26X PRO* 3.0 10.8 + - + +
28X ASP* 1.3 85.6 - - + +
30X LYS* 1.3 56.6 + - + +
32X VAL* 3.5 1.7 + - - -
33X LYS* 2.9 29.0 + - - +
201X 1VO 3.3 76.0 - - + +
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Residues in contact with LYS 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X PRO* 3.0 35.3 + - - +
27X ASN* 2.8 34.1 + - - +
28X ASP 3.3 0.2 - - - -
29X LEU* 1.3 73.6 - - + +
31X HIS* 1.3 60.5 + - - +
33X LYS* 3.3 9.9 + - + +
34X LYS* 2.9 31.4 + - - +
145X LYS* 6.1 0.4 - - - +
146X ASN* 4.3 2.8 - - - +
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Residues in contact with HIS 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X LEU* 5.4 2.0 - - + -
27X ASN 2.9 14.6 + - - +
28X ASP* 3.3 11.0 + - - +
30X LYS* 1.3 77.1 - - - +
32X VAL* 1.3 61.5 + - + +
34X LYS* 3.7 5.1 - - - +
35X LEU* 3.0 60.8 + - + +
110X TYR* 4.6 13.0 - + - +
111X ILE 5.1 2.8 + - - -
112X THR* 3.6 11.8 + - - -
152X PHE* 3.5 53.5 - + + +
153X LEU 5.7 1.0 + - - -
201X 1VO 5.2 1.3 - - - -
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Residues in contact with VAL 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X LEU* 4.0 17.8 - - + +
28X ASP* 3.0 14.6 + - - +
29X LEU* 3.7 5.4 - - - +
31X HIS* 1.3 76.9 - - + +
33X LYS* 1.3 60.4 + - - +
35X LEU* 3.5 2.5 + - - +
36X SER* 2.8 37.7 + - - +
55X LEU* 5.0 1.6 - - + -
93X PHE* 3.4 33.4 - - + -
201X 1VO 3.2 60.3 - - + +
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Residues in contact with LYS 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X LEU 2.9 19.0 + - - +
30X LYS* 3.5 11.0 - - + +
31X HIS 3.3 0.2 - - - -
32X VAL* 1.3 76.8 - - - +
34X LYS* 1.3 58.2 + - - +
36X SER* 4.0 0.2 + - - -
37X THR* 2.6 35.5 + - - +
56X PRO* 5.7 9.0 - - - -
57X ASN* 6.1 2.9 - - - +
58X ARG* 3.5 34.3 + - - +
201X 1VO 4.7 7.0 - - + -
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Residues in contact with LYS 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X LYS 2.9 17.7 + - - +
31X HIS* 3.7 5.8 - - - +
33X LYS* 1.3 77.6 - - - +
35X LEU* 1.3 63.0 + - + +
36X SER 3.4 0.2 + - - -
37X THR* 3.7 13.3 + - - +
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Residues in contact with LEU 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X LEU* 3.6 29.6 - - + -
31X HIS* 3.0 52.6 + - + +
32X VAL 4.0 2.9 - - - +
34X LYS* 1.3 77.9 - - + +
36X SER* 1.3 57.8 + - - +
39X HIS* 3.4 18.5 + - - -
91X PHE* 3.6 15.9 - - + -
110X TYR* 3.7 37.5 - - + +
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Residues in contact with SER 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X LEU* 4.5 5.2 - - - -
32X VAL* 2.8 24.1 + - - +
35X LEU* 1.3 75.9 - - - +
37X THR* 1.3 61.6 + - - +
38X GLY 3.2 0.3 + - - -
39X HIS* 2.8 29.1 + - - +
41X LEU* 3.5 34.2 - - - +
58X ARG* 3.6 25.0 + - - +
91X PHE* 4.2 11.9 - - - -
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Residues in contact with THR 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X LYS* 2.6 26.2 + - - +
34X LYS* 3.7 9.9 + - - +
35X LEU 3.6 1.8 - - - -
36X SER* 1.3 72.6 - - - +
38X GLY* 1.3 60.9 + - - +
39X HIS* 3.2 18.6 + - - -
57X ASN* 3.9 14.6 - - + +
58X ARG* 2.8 21.2 + - - +
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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