Contacts of the helix formed by residues 22 - 34 (chain h) in PDB entry 5GJQ
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 22 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416K PHE* 4.8 4.7 - - + -
417K TYR* 2.8 15.5 + - - +
14h THR* 4.1 7.6 - - - +
15h ILE 3.3 31.4 - - - +
16h PHE* 3.8 14.1 - - + -
21h ARG* 1.3 75.5 - - - +
23h TYR* 1.3 66.8 + - - +
24h GLN 3.3 2.2 - - - +
25h VAL* 3.2 32.7 + - + +
26h GLU 3.5 3.5 + - - -
126h THR* 4.0 15.0 - - + +
78i MET* 3.0 33.9 - - + -
127i ARG* 3.7 30.5 - - - +
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Residues in contact with TYR 23 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4h GLY* 3.6 11.1 - - - -
5h SER 3.6 9.1 + - - -
10h ASP* 3.4 29.0 + - - +
11h ARG* 3.1 49.6 + - + -
13h ILE 5.4 0.8 + - - -
15h ILE 4.9 0.4 + - - -
17h SER* 3.6 24.7 - - - -
19h GLU* 3.5 18.5 + - - -
21h ARG* 3.4 32.7 + - + -
22h LEU* 1.3 73.2 - - - +
24h GLN* 1.3 63.4 + - - +
26h GLU* 3.1 22.6 + - - +
27h TYR* 3.0 53.3 + + + +
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Residues in contact with GLN 24 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11h ARG 3.1 20.0 + - - +
12h HIS* 2.9 36.5 + - - +
13h ILE* 3.9 14.5 + - - +
14h THR* 3.9 21.3 - - + +
22h LEU 3.3 0.6 - - - -
23h TYR* 1.3 77.0 - - - +
25h VAL* 1.3 57.7 + - - +
27h TYR* 3.3 8.2 + - - +
28h ALA* 2.9 25.8 + - - +
132h ARG* 4.9 2.6 - - - +
133h PRO* 4.9 5.1 - - + +
12n SER 4.1 4.6 - - - +
13n THR* 3.5 8.8 - - - +
14n PHE* 3.0 56.5 + - - +
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Residues in contact with VAL 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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416K PHE* 3.1 27.8 - - + -
14h THR* 4.6 13.5 - - + -
22h LEU* 3.5 33.9 - - + +
23h TYR 3.1 0.6 - - - -
24h GLN* 1.3 73.8 - - - +
26h GLU* 1.3 57.1 + - - +
28h ALA* 2.9 19.3 + - - +
29h PHE* 2.7 31.9 + - + -
126h THR* 3.9 15.7 - - - +
133h PRO* 4.7 5.6 - - + -
156h PRO 4.5 2.9 - - - +
157h ALA* 3.4 26.0 - - + +
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Residues in contact with GLU 26 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414K HIS* 3.4 36.8 + - + +
416K PHE* 4.1 2.7 - - + -
417K TYR* 2.7 42.8 + - + +
21h ARG* 2.7 24.8 + - - -
22h LEU 3.6 3.8 - - - +
23h TYR* 3.1 36.1 + - - +
25h VAL* 1.3 76.4 - - - +
27h TYR* 1.3 70.3 + - + +
29h PHE* 3.2 7.3 + - - +
30h LYS* 3.1 24.2 + - - +
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Residues in contact with TYR 27 (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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11h ARG* 3.3 48.1 + - + +
21h ARG* 6.2 0.4 - - - -
23h TYR* 3.0 39.2 + + + -
24h GLN* 3.5 11.0 - - - +
25h VAL 3.1 0.2 - - - -
26h GLU* 1.3 86.0 - - + +
28h ALA* 1.3 56.0 + - - +
30h LYS* 3.2 12.9 + - + +
31h ALA* 2.9 21.7 + - - +
14n PHE* 4.0 16.8 - - + -
15n SER 3.6 12.3 - - - +
16n PRO* 3.1 53.9 - - + +
18n GLY* 3.3 12.4 - - - -
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Residues in contact with ALA 28 (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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24h GLN 2.9 9.9 + - - +
25h VAL* 2.9 12.0 + - - +
27h TYR* 1.3 73.8 - - - +
29h PHE* 1.3 66.7 + - - +
31h ALA* 2.9 14.8 + - - +
32h ILE* 3.1 15.6 + - - +
133h PRO* 4.2 10.3 - - + -
134h LEU 4.4 2.2 - - - +
135h GLY* 4.1 3.1 - - - -
156h PRO* 4.1 19.7 - - + -
14n PHE* 3.3 31.9 - - + -
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Residues in contact with PHE 29 (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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414K HIS* 4.0 27.6 - + + +
415K GLU* 5.5 2.5 - - + -
416K PHE* 3.3 38.1 - + - -
25h VAL* 2.7 41.7 + - + -
26h GLU* 3.3 10.8 - - - +
28h ALA* 1.3 79.0 - - - +
30h LYS* 1.3 61.7 + - + +
32h ILE* 3.2 29.8 + - + +
33h ASN* 4.1 8.0 + - - -
155h ASP* 3.9 27.4 - - + -
156h PRO* 3.9 24.9 - - + -
157h ALA* 4.0 4.3 - - + -
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Residues in contact with LYS 30 (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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383L LYS* 5.2 9.5 - - - +
26h GLU 3.1 16.0 + - - +
27h TYR* 3.5 17.9 - - + +
28h ALA 3.1 0.2 - - - -
29h PHE* 1.3 73.8 - - + +
31h ALA* 1.3 64.8 + - - +
32h ILE 3.2 1.2 + - - -
33h ASN* 3.2 19.6 + - - +
34h GLN* 3.9 10.4 + - - +
16n PRO* 2.2 42.7 + - - +
17n ASP* 4.1 14.9 + - - +
18n GLY* 4.0 7.4 - - - -
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Residues in contact with ALA 31 (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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27h TYR 2.9 12.7 + - - +
28h ALA* 2.9 12.3 + - - +
30h LYS* 1.3 78.7 - - - +
32h ILE* 1.3 60.8 + - - +
33h ASN 3.4 0.3 + - - -
34h GLN* 3.4 15.5 + - - +
35h GLY 4.7 0.3 + - - -
83h MET* 3.8 20.6 + - - +
135h GLY* 4.4 2.7 - - - -
14n PHE* 3.7 21.5 - - + -
18n GLY* 3.1 28.9 - - - +
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Residues in contact with ILE 32 (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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28h ALA 3.1 10.2 + - - +
29h PHE* 3.3 20.9 - - + +
30h LYS 3.1 0.4 - - - -
31h ALA* 1.3 78.5 - - - +
33h ASN* 1.3 71.6 + - - +
34h GLN 3.2 1.0 + - - -
35h GLY* 3.6 5.4 + - - -
36h GLY 5.0 0.2 + - - -
81h THR* 3.4 34.8 - - + +
82h GLY* 3.2 21.5 + - - -
135h GLY 4.0 14.4 - - - -
136h CYS 3.9 0.7 - - - +
137h CYS* 3.7 25.6 - - + -
156h PRO* 3.8 23.6 - - + -
168h ALA* 5.9 0.2 - - + -
169h GLY* 4.7 4.2 - - - +
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Residues in contact with ASN 33 (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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29h PHE 4.2 11.0 + - - -
30h LYS* 3.2 12.2 + - - +
32h ILE* 1.3 77.7 - - - +
34h GLN* 1.3 58.7 + - - +
35h GLY 3.1 3.1 - - - -
36h GLY* 2.9 24.2 + - - +
169h GLY* 2.9 39.8 + - - +
170h VAL* 3.9 15.6 + - + +
172h GLN* 5.9 0.2 + - - -
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Residues in contact with GLN 34 (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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30h LYS 3.9 7.4 + - - +
31h ALA 3.5 11.4 - - - +
32h ILE 3.2 1.2 - - - -
33h ASN* 1.3 77.3 - - - +
35h GLY* 1.3 60.5 + - - +
36h GLY* 3.2 0.9 + - - -
83h MET* 5.7 3.4 - - + -
17n ASP* 2.6 31.7 + - - +
18n GLY 3.5 19.3 - - - +
19n ARG* 3.7 20.8 - - + +
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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