Contacts of the helix formed by residues 13 - 24 (chain H) in PDB entry 6GYS
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 PRO 13 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11H GLU 3.6 4.5 - - - +
12H LEU* 1.3 93.7 - - + +
14H ILE* 1.3 64.4 + - + +
15H ASP 3.4 1.8 - - - +
16H ILE* 3.1 17.5 + - + +
17H ARG* 3.0 30.6 + - - +
423I ASP 4.8 10.1 - - - +
424I THR 4.7 0.9 - - - -
425I ALA* 3.7 37.7 - - + +
136K LEU* 4.8 4.3 - - + -
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Residues in contact with ILE 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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13H PRO* 1.3 77.9 - - + +
15H ASP* 1.3 64.6 + - + +
17H ARG* 3.1 20.9 - - - +
18H LYS* 2.9 29.1 + - - +
106H VAL* 3.7 27.4 - - + -
109H LEU* 3.7 28.7 - - + -
110H TYR* 4.6 12.7 + - + +
367I LEU* 5.9 4.5 - - + -
422I TYR* 5.5 15.0 - - + +
423I ASP 5.7 0.7 - - - +
424I THR* 5.4 10.1 - - - +
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Residues in contact with ASP 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H PRO* 3.4 1.0 - - - +
14H ILE* 1.3 83.7 - - + +
16H ILE* 1.3 66.3 + - + +
18H LYS* 3.9 15.1 + - - +
19H GLU* 3.6 30.9 + - - +
110H TYR* 5.4 4.0 - - - -
367I LEU* 5.4 6.0 - - + +
371I ASP* 4.1 13.7 - - - +
374I ARG* 3.3 25.7 + - - -
424I THR* 3.3 26.8 + - - +
425I ALA 5.1 0.4 - - - +
139K ASN* 3.8 17.9 + - - +
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Residues in contact with ILE 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 4.6 10.8 - - + -
12H LEU* 3.6 29.4 - - + -
13H PRO* 3.1 39.7 + - + +
15H ASP* 1.3 80.4 - - + +
17H ARG* 1.3 63.6 + - - +
19H GLU* 3.1 19.3 + - - +
20H VAL* 3.5 14.0 + - + +
425I ALA* 3.7 9.4 - - + -
135K ILE* 3.7 33.9 - - + -
136K LEU* 3.7 20.2 - - + -
139K ASN* 4.0 10.8 - - - +
147K LEU* 6.0 0.7 - - + -
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Residues in contact with ARG 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 3.3 46.6 - - + +
10H LEU* 4.0 21.4 + - - +
11H GLU 5.2 0.4 + - - -
12H LEU 2.8 24.5 + - - +
13H PRO* 3.0 12.5 + - - +
14H ILE* 3.1 41.8 + - + +
16H ILE* 1.3 76.5 - - + +
18H LYS* 1.3 61.5 + - - +
20H VAL* 3.8 6.3 + - - +
21H TYR* 3.1 25.6 + - - -
102H ASP* 2.9 40.8 + - - +
106H VAL* 4.7 3.0 - - + +
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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
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14H ILE 2.9 18.1 + - - +
15H ASP* 3.9 14.9 + - - +
16H ILE 3.2 0.2 - - - -
17H ARG* 1.3 77.4 - - - +
19H GLU* 1.3 87.3 + - + +
20H VAL 3.1 0.7 + - - -
21H TYR* 3.2 4.0 + - - +
22H PHE* 2.9 34.0 + - + -
106H VAL* 4.6 11.2 - - + +
110H TYR* 3.5 38.4 - - + -
113H THR* 6.2 4.9 - - + +
114H LEU* 3.2 22.8 - - + +
371I ASP* 4.6 13.2 + - - +
111K ARG* 5.6 5.7 - - - +
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Residues in contact with GLU 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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15H ASP* 3.6 24.3 - - - +
16H ILE* 3.1 8.3 + - - +
18H LYS* 1.3 100.2 + - + +
20H VAL* 1.3 57.5 + - - +
22H PHE* 3.2 11.9 + - + -
23H HIS* 2.8 41.8 + - + +
144K LYS* 4.8 10.7 - - - +
147K LEU* 3.3 37.6 - - - +
148K ASP* 5.6 0.7 + - - -
151K CYS* 3.4 14.0 - - - +
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 3.6 32.1 - - + -
16H ILE* 3.7 15.0 - - + +
17H ARG 4.1 1.6 - - - +
18H LYS 3.2 1.0 - - - -
19H GLU* 1.3 77.0 - - - +
21H TYR* 1.3 51.0 + - + +
23H HIS* 2.8 3.3 + - - -
24H LEU* 2.5 53.8 + - + +
135K ILE* 6.0 1.6 - - + -
151K CYS* 3.6 17.9 - - - +
154K VAL* 4.1 9.4 - - + -
155K ALA* 4.0 16.8 - - + +
158K ILE* 3.8 24.2 - - + -
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Residues in contact with TYR 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PHE* 4.4 7.1 - + - -
17H ARG* 3.1 26.0 - - + -
18H LYS 3.2 4.5 + - - +
20H VAL* 1.3 75.7 - - + +
22H PHE* 1.3 61.1 + - - +
24H LEU* 2.8 41.3 - - + +
28H PHE* 4.2 7.6 - + + -
99H LEU* 2.6 59.7 + - + +
100H VAL* 5.3 0.2 - - - -
102H ASP* 3.2 26.6 + - - -
103H CYS* 3.5 40.8 - - + -
106H VAL* 3.9 12.1 - - + -
114H LEU* 3.9 9.6 - - + -
115H ILE* 3.5 13.4 - - + +
158K ILE* 6.1 2.0 - - + -
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Residues in contact with PHE 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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18H LYS* 2.9 22.1 + - + +
19H GLU* 3.3 17.5 - - + +
21H TYR* 1.3 76.1 - - - +
23H HIS* 1.3 95.7 + + - +
24H LEU 4.9 0.4 - - - -
25H ASP* 5.2 0.5 + - - +
113H THR* 3.8 24.0 - - + -
114H LEU* 3.5 12.0 - - + +
115H ILE* 4.8 0.7 - - - -
107K ASP 4.8 2.2 - - - -
111K ARG* 3.5 43.1 - - - -
112K LYS* 2.1 68.4 + - + +
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Residues in contact with HIS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H GLU* 2.8 26.7 + - + +
20H VAL 2.8 6.3 + - - +
22H PHE* 1.3 113.1 + + - +
24H LEU* 1.3 56.2 + - - +
25H ASP* 3.8 2.4 + - - +
111K ARG* 3.1 28.0 + - + +
112K LYS* 3.8 15.0 + - - +
148K ASP* 2.9 37.1 + - - +
151K CYS* 3.5 19.3 - - + -
152K LYS* 3.9 19.1 - - + +
155K ALA* 3.4 12.6 - - + +
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Residues in contact with LEU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H VAL* 2.5 55.0 + - + +
21H TYR* 2.8 37.6 - - + +
23H HIS* 1.3 71.2 - - - +
25H ASP* 1.3 65.3 + - - +
26H GLY 3.8 0.7 - - - -
27H ASN* 4.6 3.6 - - - +
28H PHE* 3.3 34.4 - - + -
155K ALA* 3.7 17.0 - - + +
158K ILE* 4.6 10.8 - - + -
159K ARG* 3.7 42.0 - - + +
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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