Contacts of the helix formed by residues 29 - 40 (chain B) in PDB entry 3GTL
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 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B PRO 5.4 0.2 - - - +
25B ILE* 3.6 12.1 - - + -
26B THR* 2.8 30.3 + - - +
28B GLU* 1.3 84.6 - - - +
30B SER* 1.3 55.1 + - - +
32B ALA* 2.7 23.3 + - - +
33B VAL 3.6 0.5 + - - -
655B LYS* 4.2 13.3 - - - +
658B ILE* 3.1 49.3 - - + +
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Residues in contact with SER 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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25B ILE* 4.3 8.6 - - - +
26B THR 4.1 0.4 + - - -
27B ALA* 2.6 27.9 + - - +
29B ASP* 1.3 71.3 - - - +
31B TRP* 1.3 56.5 + - - +
32B ALA 3.4 0.2 - - - -
33B VAL* 3.5 12.5 + - - +
34B ILE* 2.9 30.3 + - - +
638B PHE* 4.5 11.7 - - - -
658B ILE* 5.1 0.2 - - - -
707B PRO* 5.1 6.1 - - - -
743B ILE* 3.1 27.3 + - - +
744B HIS* 3.7 18.4 + - - +
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Residues in contact with TRP 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 ALA 4.7 0.9 - - - -
28B GLU* 2.9 24.0 + - - +
29B ASP 2.8 1.0 + - - -
30B SER* 1.3 78.6 + - - +
32B ALA* 1.3 65.0 + - - +
34B ILE* 3.7 31.0 - - + -
35B SER* 3.0 19.9 + - - -
541B LEU* 6.2 0.2 - - + -
744B HIS* 3.1 44.0 + + - -
746B SER* 3.4 17.5 - - - -
747B MET* 4.8 8.1 - - - -
807B ARG* 2.7 86.1 - - + +
808B ALA* 5.4 2.9 - - + -
811B TYR* 3.3 26.0 + + - +
1045B SER* 5.5 2.0 - - - -
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Residues in contact with ALA 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 GLU 4.3 0.2 + - - -
29B ASP* 2.7 19.1 + - - +
31B TRP* 1.3 71.3 - - - +
33B VAL* 1.3 54.9 + - - +
35B SER* 2.7 29.3 + - - -
36B ALA* 2.9 13.1 + - - +
658B ILE* 3.6 23.3 - - + +
661B LEU* 5.1 7.4 - - + +
662B MET* 4.4 21.5 - - + -
665B GLU* 4.7 7.7 - - - +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 5.7 2.0 - - + -
29B ASP 3.6 1.3 + - - +
30B SER* 3.5 8.0 + - - +
31B TRP 3.4 0.2 - - - -
32B ALA* 1.3 77.7 - - - +
34B ILE* 1.3 62.8 + - - +
36B ALA* 3.1 19.1 + - - +
37B PHE* 3.1 13.0 + - - +
542B MET* 5.5 0.2 - - + -
638B PHE* 3.2 44.2 - - + -
653B VAL* 5.1 7.0 - - + -
658B ILE* 4.3 13.7 - - + -
661B LEU* 4.1 18.8 - - + +
681B TRP* 3.8 21.6 - - + -
684B LEU* 4.7 9.6 - - + -
743B ILE* 4.4 5.6 - - + -
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Residues in contact with ILE 34 (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 SER 2.9 25.2 + - - +
31B TRP* 3.7 23.8 - - + +
32B ALA 3.2 0.2 - - - -
33B VAL* 1.3 74.3 - - - +
35B SER* 1.3 53.1 + - - +
37B PHE* 2.7 30.0 + - - +
38B PHE* 3.4 10.2 - - + -
542B MET* 3.6 17.5 - - + -
743B ILE* 3.5 24.7 - - + -
744B HIS* 3.9 13.0 - - + -
747B MET* 3.7 38.6 - - + -
811B TYR* 3.5 24.0 - - + -
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Residues in contact with SER 35 (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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31B TRP 3.0 10.5 + - - -
32B ALA* 2.7 17.9 + - - -
34B ILE* 1.3 71.1 - - - +
36B ALA* 1.3 54.0 + - - +
37B PHE 2.5 15.8 - - - +
38B PHE* 4.4 1.2 - - - +
39B ARG* 3.4 26.0 + - - +
665B GLU* 4.0 21.1 + - - -
810B GLU* 5.3 0.5 + - - +
811B TYR* 3.0 35.6 + - - -
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Residues in contact with ALA 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 ALA 2.9 9.6 + - - +
33B VAL* 3.2 13.2 - - - +
35B SER* 1.3 73.5 - - - +
37B PHE* 1.3 66.5 + - - +
39B ARG* 3.5 21.9 - - - +
40B GLU* 3.5 8.0 + - - +
661B LEU* 3.7 30.7 - - + -
680B THR* 4.9 0.7 - - - -
681B TRP* 3.9 23.3 + - + +
684B LEU* 4.6 2.5 - - + -
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Residues in contact with PHE 37 (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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33B VAL 3.1 3.5 + - - +
34B ILE 2.7 16.7 - - - +
35B SER 2.5 25.1 - - - +
36B ALA* 1.3 77.1 - - - +
38B PHE* 1.3 101.3 + + - +
40B GLU* 4.9 0.9 - - + -
41B LYS* 3.9 33.0 - - + -
42B GLY 5.5 0.4 - - - -
541B LEU 4.9 1.8 - - - -
542B MET* 3.9 45.3 - - + -
543B SER 4.8 0.7 - - - -
544B CYS* 4.6 11.7 - - - -
636B PRO* 5.3 4.5 - - + -
681B TRP* 3.3 57.6 - + + -
692B TYR* 4.4 3.8 - + - -
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Residues in contact with PHE 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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34B ILE* 3.4 23.1 - - + -
35B SER 4.4 1.3 - - - +
36B ALA 3.6 0.4 + - - -
37B PHE* 1.3 106.4 - + - +
39B ARG* 1.3 62.5 + - - +
40B GLU 2.9 3.5 - - - +
41B LYS 3.9 5.4 - - - +
42B GLY* 2.6 51.4 + - - +
43B LEU* 3.2 27.4 - - + -
496B ARG* 6.1 0.2 - - - -
541B LEU* 4.1 22.2 - - + -
747B MET* 3.9 17.5 - - + -
811B TYR* 3.7 43.5 - + + -
812B LEU* 6.4 0.4 - - + -
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Residues in contact with ARG 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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35B SER* 3.4 23.6 - - - +
36B ALA* 3.5 13.0 - - - +
37B PHE 3.2 1.6 + - - -
38B PHE* 1.3 76.5 - - - +
40B GLU* 1.3 59.9 + - - +
664B THR* 4.4 13.5 + - - +
665B GLU* 4.5 21.3 + - - +
668B ASP* 3.2 42.9 + - - +
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Residues in contact with GLU 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 ALA 3.5 8.3 + - - +
37B PHE* 4.9 0.2 - - - -
38B PHE 2.9 2.6 - - - +
39B ARG* 1.3 82.2 - - + +
41B LYS* 1.3 71.7 + - + +
42B GLY 3.4 1.1 + - - -
680B THR* 3.7 10.5 + - - +
681B TRP* 3.0 47.0 - - + +
682B SER* 3.2 35.6 + - - -
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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