Contacts of the helix formed by residues 11 - 26 (chain H) in PDB entry 2GTL
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 11 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G GLY* 4.4 29.8 - - - +
35G PHE* 5.0 0.7 - - - +
37G ARG* 5.7 8.7 - - - +
38G LEU* 4.9 9.6 - - + -
10H LEU* 1.3 85.4 - - + +
12H THR* 1.3 67.3 + - + +
14H SER* 2.5 24.7 + - - -
15H LEU* 3.3 8.8 + - + +
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Residues in contact with THR 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G PHE* 4.3 16.4 - - + -
38G LEU* 3.6 28.3 - - + -
123G GLY* 6.4 0.4 - - - -
126G GLN* 3.3 29.0 + - - +
127G VAL* 3.8 27.6 - - + +
10H LEU* 3.1 10.1 - - - +
11H VAL* 1.3 73.6 - - + +
13H GLU* 1.3 66.2 + - - +
14H SER 2.6 16.3 + - - -
15H LEU* 3.0 8.6 + - + +
16H LYS* 2.9 25.2 + - - +
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G GLN* 5.4 5.6 - - + +
8H GLU* 2.6 27.8 - - - +
9H CYS* 3.7 17.7 - - - -
10H LEU* 3.0 33.1 + - + +
12H THR* 1.3 83.9 + - - +
14H SER* 1.3 55.8 + - - +
16H LYS* 4.2 3.1 - - - -
17H VAL* 3.2 25.1 + - - +
131H ASP* 5.7 0.4 - - - +
133H GLY 5.4 0.5 - - - -
134H ALA* 3.6 27.7 + - + +
137H ASP* 3.4 19.4 - - - +
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Residues in contact with SER 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H CYS* 3.9 9.8 - - - -
10H LEU 3.7 12.3 + - - -
11H VAL* 2.5 17.7 + - - +
12H THR 2.6 5.3 + - - -
13H GLU* 1.3 73.2 - - - +
15H LEU* 1.3 68.4 + - - +
16H LYS 2.9 1.3 - - - -
17H VAL* 2.5 29.5 + - - +
18H LYS* 2.7 23.0 + - - +
84H LEU* 4.1 28.5 - - - -
85H ASP* 4.9 7.7 - - - +
138H CYS* 4.4 3.1 - - - -
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PHE* 3.9 17.0 - - + -
22G LEU* 4.4 10.5 - - + -
31G ILE* 3.5 57.0 - - + +
35G PHE* 5.6 5.4 - - + +
127G VAL* 4.7 14.8 - - + -
11H VAL* 3.9 10.1 - - + +
12H THR* 3.0 8.7 + - + +
14H SER* 1.3 81.3 + - - +
16H LYS* 1.3 53.9 + - - +
18H LYS* 3.9 9.9 - - + -
19H LEU* 2.8 58.5 + - + +
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Residues in contact with LYS 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G PRO 3.8 10.1 + - - -
126G GLN* 3.1 28.4 + - - +
127G VAL* 3.4 19.9 - - - +
128G LEU 3.9 2.4 + - - -
129G ASP* 3.8 26.6 - - - +
12H THR 2.9 15.2 + - - +
13H GLU* 4.1 7.4 - - - +
14H SER 2.7 1.2 + - - -
15H LEU* 1.3 78.2 - - - +
17H VAL* 1.3 56.6 + - - +
19H LEU* 3.6 3.7 - - + +
20H GLN* 2.9 55.5 + - + +
129H HIS 4.8 1.2 + - - -
131H ASP* 2.9 45.3 + - + +
134H ALA* 4.3 3.8 - - + -
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Residues in contact with VAL 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLU 3.2 19.1 - - - +
14H SER* 2.5 12.7 + - - +
16H LYS* 1.3 69.6 - - - +
18H LYS* 1.3 57.9 + - - +
21H TRP* 2.7 34.0 + - - +
81H ILE* 4.0 15.9 - - + -
84H LEU* 4.6 8.1 - - + -
134H ALA* 3.9 26.7 - - + +
135H TRP* 3.4 50.0 - - + +
138H CYS* 4.0 7.2 - - + -
139H VAL* 5.0 3.4 - - + -
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Residues in contact with LYS 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E SER* 3.1 49.8 + - - +
27E PHE* 3.5 38.3 - - + +
14H SER* 2.7 29.9 + - - +
15H LEU* 3.6 17.9 - - + +
17H VAL* 1.3 73.5 - - - +
19H LEU* 1.3 62.0 + - - +
21H TRP* 3.7 4.2 - - - +
22H ALA* 3.5 12.1 + - - +
81H ILE* 3.1 38.2 + - + +
82H SER* 3.1 9.7 + - - +
84H LEU* 4.4 2.2 - - + +
85H ASP* 3.2 25.2 + - + +
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E SER* 4.7 5.2 - - - +
21G ILE* 4.3 23.8 - - + +
22G LEU* 4.5 16.2 - - + +
24G ARG* 6.1 3.6 - - + -
25G ASP* 4.4 21.8 - - + +
31G ILE* 4.9 2.0 - - + -
127G VAL 4.3 17.5 - - - +
128G LEU* 6.1 0.2 - - + -
15H LEU* 2.8 43.5 + - + +
16H LYS* 3.6 4.7 - - + +
18H LYS* 1.3 76.7 - - + +
20H GLN* 1.3 68.1 + - + +
22H ALA* 2.9 24.5 + - + +
23H SER* 3.5 5.9 + - - -
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Residues in contact with GLN 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G ASP* 3.7 25.1 - - - +
16H LYS* 2.9 32.4 + - + +
19H LEU* 1.3 71.7 - - + +
21H TRP* 1.3 67.2 + - - +
22H ALA 3.2 0.3 + - - -
23H SER* 3.2 6.5 + - - +
24H ALA* 3.0 23.9 + - - +
126H LEU* 3.2 30.7 - - + +
129H HIS* 3.3 11.7 - - - +
130H PHE* 3.4 2.6 - - - -
131H ASP* 3.2 31.5 + - - +
135H TRP* 2.8 31.9 - - - +
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Residues in contact with TRP 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E SER* 6.1 3.4 - - - -
17H VAL 2.7 21.9 + - - +
18H LYS 3.7 6.3 - - - +
20H GLN* 1.3 72.5 - - - +
22H ALA* 1.3 66.9 - - - +
24H ALA* 4.6 0.7 - - - -
25H PHE* 2.8 72.0 + + + +
34H PHE* 4.0 8.5 - + - -
74H LEU* 3.8 31.4 - - + -
77H LEU* 3.9 18.4 - - + -
78H ASP* 3.3 34.0 + - - +
81H ILE* 3.7 26.2 - - + -
118H LEU* 4.4 3.4 - - + -
122H LEU* 3.9 22.4 - - + -
135H TRP* 3.6 25.0 - + + -
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Residues in contact with ALA 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E SER* 5.4 8.1 - - - +
18H LYS 3.5 9.3 + - - +
19H LEU* 2.9 16.0 + - + +
21H TRP* 1.3 84.9 - - - +
23H SER* 1.3 64.4 + - - +
25H PHE* 4.2 1.3 - - - +
26H GLY* 3.1 20.8 + - - +
27H HIS* 5.1 7.6 - - + -
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Residues in contact with SER 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU 3.5 5.5 + - - -
20H GLN* 3.2 9.3 + - - -
22H ALA* 1.3 79.6 - - - +
24H ALA* 1.3 63.6 + - - +
26H GLY* 4.0 6.1 + - - -
125H ARG* 5.7 0.3 - - - -
126H LEU* 4.2 13.0 - - - -
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Residues in contact with ALA 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H GLN 3.0 16.0 + - - +
21H TRP 3.9 1.8 - - - +
23H SER* 1.3 77.2 - - - +
25H PHE* 1.3 69.8 + - - +
26H GLY* 4.3 0.2 - - - -
34H PHE* 3.9 12.1 - - - -
122H LEU* 3.5 30.5 - - + -
125H ARG* 4.0 26.3 + - + +
126H LEU* 3.9 18.4 - - + +
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Residues in contact with PHE 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E LEU* 6.3 1.3 - - + -
21H TRP* 2.8 58.6 + + + +
22H ALA* 4.2 1.1 - - - +
24H ALA* 1.3 77.3 - - - +
26H GLY* 1.3 60.9 + - - +
30H GLU* 3.9 15.1 - - - +
31H ARG* 2.9 73.5 - - + +
34H PHE* 4.4 14.9 - + - +
71H GLN* 4.3 4.7 - - - -
74H LEU* 3.6 41.5 - - + -
75H SER* 4.7 3.1 - - - -
78H ASP* 4.1 13.7 - - + -
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Residues in contact with GLY 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H ALA 3.1 15.0 + - - +
23H SER 4.3 6.1 - - - -
24H ALA 3.4 0.4 - - - -
25H PHE* 1.3 81.3 - - - +
27H HIS* 1.3 80.4 + - - -
30H GLU* 4.4 11.9 - - - -
31H ARG* 3.0 21.7 + - - -
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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