Contacts of the helix formed by residues 17 - 28 (chain a) in PDB entry 5GAH
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 17 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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968A C 3.5 33.0 - - - +
82B U 3.8 39.0 - - - +
83B G 4.1 19.0 + - - +
16a ARG* 1.3 77.3 - - - +
18a PRO* 1.3 74.0 - - + +
19a LYS* 4.2 7.0 - - + +
20a HIS* 2.8 39.5 + - + +
21a LYS* 3.2 9.6 + - - +
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Residues in contact with PRO 18 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968A C 3.7 18.6 - - - +
969A G 3.5 20.2 - - - +
16a ARG 3.6 1.3 - - - +
17a LEU* 1.3 98.3 - - + +
19a LYS* 1.3 56.8 + - + +
21a LYS* 3.4 11.1 + - + +
22a ALA* 2.9 28.8 + - - +
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Residues in contact with LYS 19 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A U 4.0 28.7 - - - +
851A C 3.9 24.8 + - - +
920A A 2.6 33.8 + - - +
921A C 3.8 23.4 + - - -
17a LEU* 3.1 5.5 + - + -
18a PRO* 1.3 80.1 - - + +
20a HIS* 1.3 63.6 + - + +
22a ALA* 3.5 7.2 + - - +
23a THR* 2.7 37.1 + - - -
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Residues in contact with HIS 20 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B U 3.3 48.3 + - - -
83B G 4.1 5.1 + - - -
16a ARG* 4.1 14.7 - - + +
17a LEU* 2.8 28.5 + - + +
19a LYS* 1.3 86.5 - - + +
21a LYS* 1.3 59.6 + - - +
22a ALA 3.2 0.4 - - - -
23a THR* 3.2 6.2 + - - -
24a LEU* 2.9 33.7 + - - +
50a ALA* 4.0 18.6 + - + +
51a VAL* 4.0 11.2 - - + +
53a PHE* 3.5 25.9 - + + -
54a MET* 5.3 1.8 - - - -
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Residues in contact with LYS 21 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969A G 5.5 5.8 + - - -
970A U 4.2 10.1 + - - -
13a ALA* 3.6 35.0 + - + +
14a ILE* 4.9 1.8 - - - +
15a GLY* 4.0 11.9 - - - +
16a ARG* 3.9 22.9 - - + +
17a LEU 3.2 8.6 + - - +
18a PRO* 3.9 10.5 - - + +
20a HIS* 1.3 75.7 - - - +
22a ALA* 1.3 58.4 + - - +
24a LEU* 3.8 7.1 - - + +
25a LEU* 3.0 31.7 + - - +
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Residues in contact with ALA 22 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A A 3.3 26.8 + - - +
850A U 3.7 20.2 - - - +
18a PRO 2.9 18.0 + - - +
19a LYS* 3.6 6.5 - - - +
21a LYS* 1.3 79.3 - - - +
23a THR* 1.3 55.2 + - - +
25a LEU* 3.9 10.0 - - - +
26a GLY* 2.9 22.3 + - - -
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Residues in contact with THR 23 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A U 3.0 28.4 + - - +
851A C 4.7 1.7 + - - -
19a LYS 2.7 22.6 + - - -
20a HIS* 3.6 6.0 - - - -
21a LYS 3.1 0.6 - - - -
22a ALA* 1.3 76.3 - - - +
24a LEU* 1.3 59.9 + - - +
26a GLY* 2.9 1.6 + - - -
27a LEU* 2.9 34.1 + - + +
47a MET* 3.3 35.2 - - + +
50a ALA* 4.5 11.1 - - + +
51a VAL* 4.0 15.3 - - + -
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Residues in contact with LEU 24 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9a GLN* 3.8 15.3 - - - +
13a ALA* 3.8 17.3 - - + -
16a ARG* 5.6 0.7 - - + -
20a HIS* 2.9 21.7 + - + +
21a LYS* 3.8 6.3 - - + +
23a THR* 1.3 77.0 - - - +
25a LEU* 1.3 60.3 + - - +
27a LEU* 3.3 4.1 + - + +
28a GLY 3.1 3.6 + - - -
29a LEU* 2.9 51.8 + - + +
51a VAL* 4.1 13.2 - - + -
54a MET* 3.6 32.8 - - + -
55a VAL* 3.9 28.5 - - + -
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Residues in contact with LEU 25 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A A 4.6 13.0 - - + +
929A U 3.0 17.6 + - - +
930A G 4.1 47.1 - - - +
21a LYS 3.0 17.8 + - - +
22a ALA* 4.1 8.3 - - - +
24a LEU* 1.3 74.8 - - - +
26a GLY* 1.3 69.8 + - - +
28a GLY* 3.1 6.9 + - - +
29a LEU 4.7 3.6 + - - +
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Residues in contact with GLY 26 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849A A 5.5 1.1 - - - -
850A U 4.2 16.6 - - - -
928A A 4.0 8.7 + - - +
929A U 3.3 32.4 - - - +
22a ALA 2.9 18.5 + - - -
23a THR* 2.9 8.0 + - - -
25a LEU* 1.3 79.4 - - - +
27a LEU* 1.3 57.6 + - - +
38a ARG* 5.9 0.2 - - - -
47a MET* 4.2 6.9 - - - +
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Residues in contact with LEU 27 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929A U 3.9 1.8 - - - -
7a ILE* 4.6 16.2 - - + -
23a THR* 2.9 33.7 + - + +
24a LEU* 3.8 8.3 - - + +
25a LEU 3.1 0.2 - - - -
26a GLY* 1.3 77.9 - - - +
28a GLY* 1.3 59.6 + - - +
29a LEU* 4.5 19.1 - - + +
36a VAL* 3.8 9.4 - - + +
38a ARG* 2.9 33.1 + - + +
44a ILE* 4.5 18.6 - - + +
47a MET* 3.6 37.2 - - + +
48a ILE* 4.8 3.4 - - + +
51a VAL* 4.1 17.7 - - + -
55a VAL* 5.3 1.1 - - + -
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Residues in contact with GLY 28 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929A U 3.4 17.7 + - - -
930A G 5.0 5.6 - - - -
24a LEU 3.1 0.4 + - - -
25a LEU* 3.1 12.9 + - - -
27a LEU* 1.3 79.6 - - - +
29a LEU* 1.3 61.2 + - - +
30a ARG* 3.6 10.9 + - - +
34a HIS* 3.6 9.2 - - - -
36a VAL* 3.6 17.0 - - - +
38a ARG* 4.4 6.7 - - - -
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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
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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