Contacts of the helix formed by residues 44 - 56 (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 VAL 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 1.3 87.2 - - - +
45B SER* 1.3 70.2 + - - +
46B GLN* 3.3 10.3 - - - +
47B GLN* 2.9 22.2 + - + +
48B LEU* 3.4 21.0 + - + -
199B MET* 3.2 41.3 - - + +
201B GLY* 4.6 6.3 - - - +
492B LEU* 5.0 2.2 - - + -
495B LEU* 3.3 42.2 - - + -
496B ARG* 4.9 4.5 - - + -
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.1 36.1 + - - -
43B LEU 3.6 1.8 - - - -
44B VAL* 1.3 73.7 - - - +
46B GLN* 1.3 76.1 + - - +
48B LEU* 2.5 40.8 + - - +
49B ASP* 2.6 32.2 + - - -
544B CYS* 4.2 15.6 - - - -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.9 9.8 - - - +
45B SER* 1.3 83.2 + - - +
47B GLN* 1.3 82.5 + - - +
49B ASP* 3.8 6.7 - - - +
50B SER* 3.0 30.7 + - - -
408B LEU* 3.3 19.5 - - + +
495B LEU 3.8 2.2 + - - -
496B ARG* 3.5 52.9 - - - +
539B LEU* 4.1 18.3 - - + +
543B SER 4.8 1.6 - - - +
544B CYS* 4.5 3.8 - - - -
545B ILE* 4.2 34.1 - - + +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 2.9 17.7 + - + +
45B SER 2.7 2.6 + - - -
46B GLN* 1.3 88.5 + - - +
48B LEU* 1.3 50.3 + - - +
50B SER* 3.0 5.1 + - - -
51B PHE 2.8 30.7 + - - -
173B MET* 3.4 26.7 - - + +
201B GLY* 3.4 27.2 - - - +
211B VAL* 4.5 4.1 - - - +
212B LEU* 3.4 26.8 + - - +
214B ALA* 5.0 4.0 - - - +
408B LEU* 3.8 17.0 - - - +
409B ALA* 3.8 8.6 - - - +
495B LEU* 3.0 26.1 + - + +
497B ARG 5.3 1.6 + - - -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS 5.3 3.1 - - - +
42B GLY* 6.3 0.7 - - - -
43B LEU 6.2 0.2 - - - +
44B VAL* 4.0 22.4 - - + +
45B SER* 2.5 24.3 + - - +
47B GLN* 1.3 69.7 - - + +
49B ASP* 1.3 65.8 + - - +
50B SER 2.8 5.5 + - - -
51B PHE* 3.1 0.6 + - - -
52B ASN* 2.9 38.0 + - - +
173B MET* 3.5 16.8 - - + -
174B LEU 4.4 2.9 - - - +
175B ARG* 3.3 33.9 - - + +
176B SER* 3.8 15.9 - - - +
199B MET 4.9 2.9 - - - +
201B GLY 4.9 2.9 - - - +
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Residues in contact with ASP 49 (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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41B LYS* 4.4 18.3 + - - +
45B SER* 2.6 43.3 + - - +
46B GLN* 3.8 6.9 + - - +
48B LEU* 1.3 74.4 - - - +
50B SER* 1.3 59.3 + - - +
52B ASN* 4.1 8.4 + - - +
53B GLN* 3.5 9.5 + - - +
544B CYS* 5.1 3.3 - - + +
545B ILE 5.4 5.2 - - - +
547B VAL* 3.2 31.3 - - + +
634B TYR* 5.7 0.3 + - - -
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Residues in contact with SER 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 GLN 3.0 17.9 + - - -
47B GLN 3.3 4.9 - - - -
48B LEU 2.8 2.4 - - - -
49B ASP* 1.3 76.3 - - - +
51B PHE* 1.3 64.8 + - - -
52B ASN 3.2 1.1 - - - -
53B GLN* 3.4 6.6 + - - +
54B PHE* 3.1 19.6 + - - +
408B LEU* 3.5 19.7 - - - +
409B ALA 4.4 0.7 - - - -
410B GLY* 3.0 26.2 + - - -
411B PRO* 3.4 12.0 - - - +
545B ILE* 6.4 0.4 - - - -
547B VAL* 4.8 2.7 - - - -
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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
----------------------------------------------------------
47B GLN 2.8 9.8 + - - +
48B LEU 4.1 0.7 - - - +
50B SER* 1.3 73.0 - - - +
52B ASN* 1.3 58.2 + - - +
54B PHE* 3.0 15.1 + + - +
55B VAL* 2.9 48.9 + - + +
170B LEU* 4.5 3.6 - - + -
171B PRO 3.5 20.6 - - - -
172B ILE* 3.9 13.5 - - + -
173B MET* 3.6 45.8 - - + -
176B SER* 3.6 24.9 - - - -
178B ASN* 5.8 0.2 - - + -
203B PHE* 3.5 18.2 - + - -
409B ALA* 5.1 2.7 - - + -
410B GLY* 4.4 3.1 - - - +
413B LEU* 3.4 33.9 - - + -
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Residues in contact with ASN 52 (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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48B LEU* 2.9 29.0 + - - +
49B ASP* 4.1 8.4 + - - +
51B PHE* 1.3 77.5 - - - +
53B GLN* 1.3 57.0 + - - +
55B VAL* 3.3 3.2 + - - +
56B ASP* 2.9 39.9 + - - +
176B SER* 3.6 27.0 + - - -
177B LYS* 3.5 43.0 - - - +
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Residues in contact with GLN 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 ASP 3.5 4.4 + - - +
50B SER* 3.4 5.3 + - - +
51B PHE 3.4 0.4 - - - -
52B ASN* 1.3 74.8 - - - +
54B PHE* 1.3 60.8 + - - +
56B ASP* 4.4 5.2 - - - +
57B TYR* 3.8 34.5 - - - +
58B THR* 3.0 25.7 + - - +
411B PRO* 6.5 1.1 - - + -
547B VAL* 3.5 46.5 - - + +
548B GLY 3.8 16.2 + - - -
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Residues in contact with PHE 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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50B SER 3.1 12.1 + - - +
51B PHE* 3.0 27.1 + + + +
53B GLN* 1.3 77.2 - - - +
55B VAL* 1.3 71.8 + - + +
58B THR* 3.5 22.3 + - + -
59B LEU* 3.1 55.9 + - + +
62B ILE* 5.4 2.5 - - + -
170B LEU* 4.3 19.5 - - + -
410B GLY* 4.0 24.5 - - - -
411B PRO* 5.0 1.3 - - + -
413B LEU* 4.0 18.4 - - + -
414B ALA* 3.6 28.5 - - + -
417B PHE* 4.3 15.5 - + + -
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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
----------------------------------------------------------
51B PHE* 2.9 42.9 + - + +
52B ASN* 4.1 3.6 - - - +
54B PHE* 1.3 82.7 - - + +
56B ASP* 1.3 78.3 + - - +
57B TYR 3.4 0.3 + - - -
59B LEU* 3.6 23.2 - - + +
60B GLN 5.1 0.3 + - - -
95B ILE* 5.7 1.7 - - - +
97B VAL* 4.9 12.2 - - + +
170B LEU* 4.1 19.1 - - + -
172B ILE* 4.9 4.5 - - + -
177B LYS* 5.8 4.9 - - + -
178B ASN* 3.6 25.1 - - + +
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 2.9 24.2 + - - +
53B GLN* 4.9 0.7 - - - -
55B VAL* 1.3 88.7 - - - +
57B TYR* 1.3 84.8 + - + +
60B GLN* 5.4 3.5 - - - +
177B LYS* 3.9 29.4 - - - +
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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