Contacts of the helix formed by residues 30 - 42 (chain K) in PDB entry 4GGF
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 TYR 30 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C THR 2.6 30.4 + - - -
69C ASN* 4.5 7.7 - - + -
70C ALA* 4.9 0.2 - - - +
23K LYS* 3.4 25.8 - - - -
24K GLY* 3.6 2.6 - - - -
25K ASN* 3.0 19.4 + - - +
28K ALA* 3.7 18.4 - - + -
29K VAL* 1.3 74.9 - - - +
31K ARG* 1.3 61.8 + - - +
32K ASP* 3.2 12.6 - - - +
33K ASP* 3.1 28.7 + - - +
34K LEU* 2.8 26.7 + - - +
55K PHE* 3.7 1.6 - - - -
63K ASP 6.1 0.2 - - - -
64K GLY 3.6 18.6 - - - -
65K ALA* 3.9 5.8 - - + -
23S LYS* 3.6 33.0 - - + +
32S ASP* 3.8 19.1 - - - +
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Residues in contact with ARG 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K TYR* 1.3 76.3 - - - +
32K ASP* 1.3 61.3 + - - +
34K LEU* 3.4 3.6 + - - +
35K LYS* 3.4 17.3 + - - +
51K ALA* 5.3 3.7 - - - +
52K ASP* 3.3 55.7 + - - +
55K PHE* 3.4 55.7 - - + +
56K LYS* 5.2 3.2 - - - +
64K GLY 4.4 1.2 + - - -
31S ARG* 5.0 17.0 - - - +
32S ASP* 5.1 9.7 + - + +
103S GOL 6.2 2.7 - - - -
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Residues in contact with ASP 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K LYS* 3.0 32.6 + - - -
30K TYR* 3.5 14.2 - - - +
31K ARG* 1.3 73.9 - - - +
33K ASP* 1.3 69.7 + - - -
35K LYS* 3.3 17.7 + - - +
36K LYS* 3.5 10.4 + - - +
30S TYR* 3.8 20.6 - - - +
31S ARG* 6.2 0.4 - - - -
32S ASP* 5.4 2.0 - - - +
64S GLY 4.9 0.9 - - - +
103S GOL 3.5 45.7 + - - +
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Residues in contact with ASP 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR* 4.2 15.4 - - + +
22K ILE* 3.6 26.4 - - + +
23K LYS* 2.7 29.6 + - - +
28K ALA 4.3 0.7 - - - +
29K VAL* 3.6 16.5 - - + +
30K TYR* 3.1 38.9 + - - +
32K ASP* 1.3 81.8 + - - +
34K LEU* 1.3 58.7 + - - +
36K LYS* 3.1 11.7 + - - +
37K LEU* 2.9 25.8 + - - +
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Residues in contact with LEU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K VAL* 3.5 17.9 - - + +
30K TYR 2.8 19.1 + - - +
31K ARG 3.7 5.6 - - - +
32K ASP 3.3 0.2 - - - -
33K ASP* 1.3 70.8 - - - +
35K LYS* 1.3 66.4 + - - +
37K LEU* 3.3 21.4 + - + +
38K LEU* 2.9 33.2 + - + +
51K ALA 3.9 7.2 - - - +
54K TRP* 4.1 8.5 - - + -
55K PHE* 3.6 47.8 - - + +
58K LEU* 4.2 22.0 - - + -
66K VAL* 4.5 9.0 - - + -
71K PHE* 6.0 0.9 - - + -
74K LEU* 5.0 2.7 - - + -
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Residues in contact with LYS 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K ARG 3.4 7.5 + - - +
32K ASP* 3.3 13.4 + - - +
33K ASP 3.2 0.6 - - - -
34K LEU* 1.3 78.3 - - - +
36K LYS* 1.3 57.4 + - + +
38K LEU* 3.5 1.5 + - - +
39K GLU* 3.0 60.5 + - + +
51K ALA* 3.9 21.7 - - + +
101K SO4 3.0 31.8 + - - +
103S GOL 4.3 15.0 + - - +
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Residues in contact with LYS 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR* 3.9 13.6 - - + -
22K ILE* 4.7 15.9 - - + -
32K ASP 3.5 11.2 + - - +
33K ASP* 3.1 10.5 + - - +
35K LYS* 1.3 76.1 - - + +
37K LEU* 1.3 65.7 + - - +
39K GLU* 3.9 11.0 - - - +
40K THR* 3.1 31.0 + - - +
69V ASN* 3.6 28.6 - - - +
71V ASP* 5.5 4.0 - - - -
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Residues in contact with LEU 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K VAL* 5.3 0.9 - - + -
16K TYR* 4.9 4.0 - - + -
19K TYR* 3.6 46.7 - - + -
29K VAL* 4.5 10.5 - - + -
33K ASP 2.9 12.8 + - - +
34K LEU* 3.6 22.4 - - + +
36K LYS* 1.3 76.5 - - - +
38K LEU* 1.3 62.9 + - + +
41K GLU* 2.8 47.5 + - + +
42K SER* 5.9 0.7 - - - +
66K VAL* 6.5 0.2 - - + -
71K PHE* 4.0 27.8 - - + -
74K LEU* 4.0 25.1 - - + -
8L LEU* 5.0 1.6 - - + -
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Residues in contact with LEU 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K LEU* 2.9 38.5 + - + +
35K LYS* 4.0 2.7 - - - +
37K LEU* 1.3 74.2 - - + +
39K GLU* 1.3 65.3 + - + +
42K SER* 2.7 45.9 + - - +
46K ILE* 4.3 6.1 - - + -
47K ARG* 3.3 16.5 - - + +
51K ALA* 3.7 33.0 - - + +
54K TRP* 4.0 30.3 - - + -
74K LEU* 4.1 26.2 - - + -
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Residues in contact with GLU 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K LYS* 3.0 51.1 + - + +
36K LYS* 3.9 14.0 - - - +
38K LEU* 1.3 78.1 - - + +
40K THR* 1.3 60.7 + - - +
47K ARG* 3.7 27.4 + - - +
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Residues in contact with THR 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TYR* 3.3 27.1 + - - +
36K LYS* 3.1 15.7 + - - +
39K GLU* 1.3 78.4 - - - +
41K GLU* 1.3 68.7 + - - +
42K SER 3.8 0.7 - - - -
6L SER* 3.3 15.6 - - - -
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Residues in contact with GLU 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K VAL* 3.7 25.6 - - + +
18K LYS* 4.7 7.6 - - - +
19K TYR* 2.7 33.7 + - + +
37K LEU* 2.8 28.8 + - + +
40K THR* 1.3 83.4 - - - +
42K SER* 1.3 57.4 - - - +
78K MET* 4.0 2.9 - - - +
6L SER* 2.7 28.1 + - - -
7L GLN* 3.7 7.4 + - - +
8L LEU* 3.3 45.2 + - + +
9L GLU* 3.7 9.5 - - - +
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Residues in contact with SER 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K LEU* 6.1 0.7 - - - -
38K LEU* 2.7 36.8 + - - +
39K GLU 4.5 1.2 - - - +
40K THR 5.0 0.7 - - - -
41K GLU* 1.3 80.6 - - - +
43K PRO* 1.3 67.2 - - - +
46K ILE* 3.5 24.9 - - - +
47K ARG* 2.9 35.2 + - - +
74K LEU* 6.0 0.2 - - - -
78K MET* 4.1 12.6 - - - -
9L GLU* 4.6 2.9 - - - -
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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