Contacts of the helix formed by residues 11 - 26 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34K GLY* 4.4 27.6 - - - +
35K PHE* 5.0 1.6 - - - +
37K ARG* 5.8 6.7 - - - +
38K LEU* 4.2 20.6 - - + -
10L LEU* 1.3 84.5 - - + +
12L THR* 1.3 62.5 + - + +
14L SER* 2.5 24.2 + - - +
15L LEU* 3.3 9.3 + - + +
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Residues in contact with THR 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K PHE* 4.5 15.0 - - + -
38K LEU* 3.5 27.4 - - + -
123K GLY* 5.2 1.1 - - - +
126K GLN* 2.6 37.8 + - + +
127K VAL* 4.0 26.2 - - + +
10L LEU* 3.0 9.1 - - - +
11L VAL* 1.3 72.2 - - + +
13L GLU* 1.3 65.3 + - - +
14L SER 2.6 17.1 + - - -
15L LEU* 3.0 5.3 + - - +
16L LYS* 2.9 25.0 + - - +
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Residues in contact with GLU 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126K GLN* 5.2 5.8 - - + +
8L GLU* 2.6 27.0 - - - +
9L CYS* 3.8 16.4 - - - -
10L LEU* 3.0 33.7 + - + +
12L THR* 1.3 84.5 + - - +
14L SER* 1.3 56.9 + - - +
16L LYS* 4.2 3.4 - - - -
17L VAL* 3.2 24.3 + - - +
131L ASP* 5.7 0.4 - - - +
133L GLY 5.4 0.5 - - - -
134L ALA* 3.6 27.2 + - + +
137L ASP* 3.4 19.5 - - - +
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Residues in contact with SER 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L CYS* 3.9 8.2 - - - -
10L LEU 3.7 12.9 + - - -
11L VAL* 2.5 18.4 + - - +
12L THR 2.6 5.7 + - - -
13L GLU* 1.3 73.0 - - - +
15L LEU* 1.3 67.5 + - - +
16L LYS 2.9 1.1 - - - -
17L VAL* 2.5 27.9 + - - +
18L LYS* 2.7 22.9 + - - +
84L LEU* 4.1 28.5 - - - -
85L ASP* 4.9 7.8 - - - +
138L CYS* 4.4 3.4 - - - -
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Residues in contact with LEU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I PHE* 4.1 14.6 - - + -
22K LEU* 4.4 4.9 - - + -
31K ILE* 3.8 48.9 - - + -
35K PHE* 5.4 6.3 - - + -
127K VAL* 3.9 26.7 - - + -
11L VAL* 3.9 9.6 - - + +
12L THR* 3.0 8.0 + - - +
14L SER* 1.3 82.0 + - - +
16L LYS* 1.3 53.9 + - - +
18L LYS* 3.9 9.9 - - + -
19L LEU* 2.8 59.6 + - + +
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Residues in contact with LYS 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K PRO 3.6 15.8 + - - -
126K GLN* 3.0 28.4 + - - +
127K VAL* 3.7 17.4 - - - +
128K LEU 4.0 2.7 + - - -
129K ASP* 3.8 25.1 - - - +
12L THR 2.9 10.9 + - - +
13L GLU* 4.1 7.2 - - - +
14L SER 2.8 0.6 + - - -
15L LEU* 1.3 78.6 - - - +
17L VAL* 1.3 58.0 + - - +
19L LEU* 3.6 3.8 - - + +
20L GLN* 2.9 55.9 + - + +
129L HIS 4.8 1.7 + - - -
131L ASP* 2.9 46.9 + - + +
134L ALA* 4.3 4.3 - - + -
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Residues in contact with VAL 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L GLU 3.2 19.3 - - - +
14L SER* 2.5 12.5 + - - +
16L LYS* 1.3 71.3 - - - +
18L LYS* 1.3 58.4 + - - +
21L TRP* 2.7 33.8 + - - +
81L ILE* 4.1 15.9 - - + -
84L LEU* 4.7 8.1 - - + -
134L ALA* 3.8 26.2 - - + +
135L TRP* 3.4 50.5 - - + +
138L CYS* 4.0 7.2 - - + -
139L VAL* 5.0 2.7 - - + -
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Residues in contact with LYS 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I SER* 3.5 33.0 + - - +
27I PHE* 3.8 28.2 - - + +
14L SER* 2.7 29.1 + - - +
15L LEU* 3.6 24.9 - - + +
17L VAL* 1.3 72.5 - - - +
19L LEU* 1.3 65.4 + - + +
21L TRP* 3.8 4.3 - - - +
22L ALA* 3.5 14.7 + - - +
81L ILE* 3.1 39.1 + - + +
82L SER* 3.2 20.0 + - - +
84L LEU* 4.4 1.3 - - + +
85L ASP* 3.2 26.8 + - + +
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Residues in contact with LEU 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I SER* 4.8 8.7 - - - +
21K ILE* 4.5 22.0 - - + +
22K LEU* 4.5 18.4 - - + +
24K ARG* 6.4 1.8 - - + -
25K ASP* 5.0 10.8 - - - +
31K ILE* 5.1 4.5 - - + -
127K VAL 3.7 22.7 - - - +
128K LEU* 5.7 0.2 - - + -
129K ASP* 6.1 0.4 - - - +
15L LEU* 2.8 41.1 + - + +
16L LYS* 3.6 4.7 - - + +
18L LYS* 1.3 78.2 - - + +
20L GLN* 1.3 66.7 + - + +
22L ALA* 3.0 24.2 + - + +
23L SER* 3.5 6.1 + - - -
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Residues in contact with GLN 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K ASP* 3.7 29.5 - - + +
16L LYS* 2.9 31.4 + - + +
17L VAL 4.0 0.2 - - - +
19L LEU* 1.3 71.0 - - + +
21L TRP* 1.3 67.4 + - - +
22L ALA 3.1 0.2 + - - -
23L SER* 3.2 6.4 + - - +
24L ALA* 3.0 24.3 + - - +
126L LEU* 3.2 30.2 - - + +
129L HIS* 3.3 11.8 - - - +
130L PHE* 3.4 2.0 - - - -
131L ASP* 3.2 31.7 + - - +
135L TRP* 2.8 31.5 - - - +
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Residues in contact with TRP 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I SER* 6.5 0.9 - - - -
17L VAL 2.7 21.9 + - - +
18L LYS 3.8 7.0 - - - +
20L GLN* 1.3 70.7 - - - +
22L ALA* 1.3 66.2 + - - +
24L ALA* 4.6 0.7 - - - -
25L PHE* 2.8 72.1 + + + +
34L PHE* 4.1 9.6 - + - -
74L LEU* 3.8 30.7 - - + -
77L LEU* 3.9 18.6 - - + -
78L ASP* 3.3 34.6 + - - +
81L ILE* 3.8 25.4 - - + -
118L LEU* 4.4 3.8 - - + -
122L LEU* 3.9 21.3 - - + -
135L TRP* 3.6 25.5 - + + -
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Residues in contact with ALA 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I SER* 5.5 8.7 - - - +
18L LYS 3.5 9.4 + - - +
19L LEU* 3.0 15.6 + - + +
21L TRP* 1.3 84.2 - - - +
23L SER* 1.3 65.0 + - - +
25L PHE* 5.1 1.1 - - - -
26L GLY* 3.1 20.6 + - - +
27L HIS* 5.1 8.2 - - + -
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Residues in contact with SER 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129K ASP* 5.6 2.6 + - - -
19L LEU 3.5 6.1 + - - -
20L GLN* 3.2 8.0 + - - -
22L ALA* 1.3 80.1 - - - +
24L ALA* 1.3 65.3 + - - +
26L GLY* 4.0 6.2 + - - -
125L ARG* 5.7 0.3 - - - -
126L LEU* 4.2 13.0 - - - -
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Residues in contact with ALA 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L GLN 3.0 17.5 + - - +
21L TRP 3.9 1.8 - - - +
23L SER* 1.3 78.2 - - - +
25L PHE* 1.3 69.7 + - - +
26L GLY* 4.3 0.3 - - - -
34L PHE* 3.9 11.4 - - + -
122L LEU* 3.5 31.0 - - + -
125L ARG* 4.0 26.2 + - + +
126L LEU* 3.9 19.0 - - + +
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Residues in contact with PHE 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I LEU* 6.5 1.1 - - + -
21L TRP* 2.8 60.4 + + + +
22L ALA* 4.3 1.3 - - - +
24L ALA* 1.3 76.4 - - - +
26L GLY* 1.3 61.0 + - - +
30L GLU* 3.8 15.1 - - - +
31L ARG* 2.9 73.6 - - + +
34L PHE* 4.4 15.2 - + - +
71L GLN* 4.3 4.7 - - - -
74L LEU* 3.6 41.3 - - + -
75L SER* 4.7 3.6 - - - -
78L ASP* 4.0 14.6 - - + -
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Residues in contact with GLY 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ALA 3.1 14.4 + - - +
23L SER 4.3 5.4 - - - -
24L ALA 3.4 1.5 - - - -
25L PHE* 1.3 81.8 - - - +
27L HIS* 1.3 79.5 + - - -
30L GLU* 4.4 11.2 - - - -
31L ARG* 3.0 22.5 + - - -
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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