Contacts of the helix formed by residues 13 - 23 (chain H) in PDB entry 7C17
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 THR 13 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402 G 3.4 33.9 - - + +
7H ALA* 4.7 5.8 - - - -
12H LEU* 1.3 78.3 - - - +
14H SER* 1.3 69.4 + - - +
15H LYS* 3.5 17.7 + - + +
16H ALA 3.8 2.1 + - - +
17H ILE* 3.3 27.6 + - - +
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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
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461 T 4.7 23.3 - - - -
471 T 3.7 32.3 + - - +
3H ILE* 5.4 6.7 - - - -
7H ALA* 5.1 3.2 - - - +
13H THR* 1.3 81.4 + - - +
15H LYS* 1.3 57.0 + - - -
16H ALA 3.5 0.2 - - - -
17H ILE* 5.1 1.8 - - - -
18H ARG* 2.9 29.3 + - - +
37H ARG* 3.4 12.4 + - - +
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Residues in contact with LYS 15 (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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471 T 6.0 1.3 - - - +
481 C 5.5 0.2 - - - +
491 C 4.2 2.9 - - - +
501 C 4.3 2.1 - - - +
392 G 3.8 23.4 + - + -
402 G 2.7 67.7 + - + +
412 G 3.0 24.5 + - - +
13H THR* 3.3 12.1 + - + +
14H SER* 1.3 77.7 - - - +
16H ALA* 1.3 60.5 + - - +
18H ARG* 3.4 27.2 + - - +
19H PHE* 2.9 31.9 + - - +
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Residues in contact with ALA 16 (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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392 G 3.8 25.4 - - - -
402 G 3.5 19.0 + - - +
12H LEU* 4.5 22.7 - - + -
13H THR* 3.8 10.3 + - + +
14H SER 3.5 0.2 - - - -
15H LYS* 1.3 79.5 - - - +
17H ILE* 1.3 56.6 + - - +
19H PHE* 3.3 7.3 + - - +
20H TYR* 2.9 36.7 + - + -
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Residues in contact with ILE 17 (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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3H ILE* 3.7 28.0 - - + -
7H ALA* 4.9 2.5 - - + -
10H THR* 4.0 17.7 - - + -
12H LEU* 4.1 19.1 - - + -
13H THR 3.3 21.0 + - - +
14H SER* 5.1 0.7 - - - -
15H LYS 3.4 0.2 - - - -
16H ALA* 1.3 73.5 - - - +
18H ARG* 1.3 60.4 + - - +
20H TYR* 3.3 11.3 + - + +
21H GLU* 2.9 27.5 + - - +
26H VAL* 5.9 2.9 - - + +
37H ARG* 4.1 9.5 + - - +
39H TYR* 3.9 20.4 - - + +
47H LEU* 3.9 30.1 - - + -
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Residues in contact with ARG 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471 T 3.4 40.1 + - - +
481 C 3.3 37.0 + - - +
491 C 3.1 38.3 - - - +
14H SER 2.9 22.1 + - - +
15H LYS* 3.6 24.3 - - - +
16H ALA 3.3 0.2 - - - -
17H ILE* 1.3 74.4 - - - +
19H PHE* 1.3 60.3 + - - +
21H GLU* 3.2 5.6 + - - +
22H GLU* 2.9 45.7 + - + +
37H ARG* 3.4 21.0 - - - +
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Residues in contact with PHE 19 (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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362 C 6.1 2.2 - - + -
372 A 5.0 8.5 - + - -
382 A 3.5 35.9 - + + -
392 G 4.0 31.2 - + + +
15H LYS* 2.9 21.2 + - - +
16H ALA* 3.3 4.2 + - - +
18H ARG* 1.3 72.9 - - - +
20H TYR* 1.3 78.6 + + - +
22H GLU* 3.4 8.7 + - + +
23H LYS* 3.2 48.6 + - + +
60H LEU* 3.8 24.9 - - + -
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Residues in contact with TYR 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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392 G 2.7 41.0 + - - -
12H LEU* 4.0 19.6 - - + +
16H ALA* 2.9 23.8 + - + -
17H ILE* 3.5 19.5 - - + +
18H ARG 3.3 0.2 - - - -
19H PHE* 1.3 88.5 - + - +
21H GLU* 1.3 59.4 + - - +
23H LYS* 3.3 21.3 + - + +
25H LEU* 4.7 12.5 - - + +
26H VAL* 3.3 30.4 + - + +
50H LEU* 3.6 32.8 - - + -
54H ARG* 3.4 15.1 - - + +
60H LEU* 3.7 19.5 - - + -
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Residues in contact with GLU 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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471 T 3.8 2.4 + - - -
17H ILE 2.9 14.2 + - - +
18H ARG* 3.2 10.2 + - - +
20H TYR* 1.3 77.2 - - - +
22H GLU* 1.3 63.8 + - - +
23H LYS 3.3 8.1 - - - +
26H VAL* 4.3 17.8 - - + +
27H THR 5.5 0.4 - - - +
28H PRO* 5.6 1.8 - - + -
29H PRO* 3.9 23.1 - - + +
31H ARG* 2.6 31.2 + - - -
37H ARG* 3.0 38.2 + - - +
39H TYR* 4.8 3.4 - - - +
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Residues in contact with GLU 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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481 C 5.2 6.1 + - - -
18H ARG* 2.9 38.6 + - + +
19H PHE* 3.9 11.0 - - + +
20H TYR 3.3 0.4 - - - -
21H GLU* 1.3 79.7 - - + +
23H LYS* 1.3 62.5 + - + +
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Residues in contact with LYS 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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362 C 4.4 25.4 + - + +
372 A 3.2 28.8 + - - -
19H PHE* 3.2 46.8 + - + +
20H TYR* 3.3 11.8 + - + +
21H GLU 3.2 13.5 - - - +
22H GLU* 1.3 81.4 - - + +
24H GLY* 1.3 63.6 + - - +
25H LEU* 3.1 27.4 + - + -
26H VAL 4.1 5.2 + - - +
60H LEU* 5.5 4.0 - - + -
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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