Contacts of the helix formed by residues 18 - 31 (chain K) in PDB entry 1K73
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 ILE 18 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1243A C 3.4 27.4 - - - +
1244A U 2.8 49.4 - - - +
17K CYS* 1.3 70.1 - - - +
19K MET* 1.3 65.6 + - - +
21K ARG* 2.9 35.3 + - + +
22K VAL* 3.0 12.6 + - - +
45K VAL* 3.4 9.0 - - + +
46K ILE* 5.6 0.9 - - - -
47K THR* 4.5 9.6 - - - +
118K GLY 5.3 0.4 - - - +
119K THR* 2.7 19.6 + - - +
120K SER 4.9 3.4 - - - +
121K LEU* 4.5 23.1 - - + -
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Residues in contact with MET 19 (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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1242A A 5.0 3.4 - - - +
1243A C 4.0 5.8 + - - +
17K CYS 3.1 8.4 + - - -
18K ILE* 1.3 69.1 - - - +
20K GLY* 1.3 54.7 + - - +
22K VAL* 3.1 3.9 + - - +
23K ALA* 2.7 36.0 + - - +
44K ALA* 4.8 4.3 - - + -
45K VAL 3.1 14.1 + - - +
46K ILE* 4.8 5.2 - - + -
57K TYR* 4.6 10.5 - - - -
78K ILE* 3.5 15.3 - - + -
79K PHE* 3.4 53.0 - - + -
82K THR* 3.6 21.3 - - + +
132K LEU* 3.0 45.8 - - + -
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Residues in contact with GLY 20 (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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1242A A 3.1 33.6 + - - -
1243A C 2.9 15.7 + - - -
1247A A 3.5 8.6 + - - -
19K MET* 1.3 75.4 - - - +
21K ARG* 1.3 56.1 + - - +
23K ALA* 3.6 5.3 - - - +
24K SER* 2.9 31.0 + - - -
86K MET* 3.9 2.7 - - - +
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Residues in contact with ARG 21 (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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1109A U 2.7 65.9 + - + +
1243A C 3.2 28.0 + - - +
1244A U 2.7 23.8 + - - -
1246A A 3.6 16.8 + - - -
1247A A 3.1 30.8 + - - +
18K ILE* 2.9 29.7 + - + +
20K GLY* 1.3 69.1 - - - +
22K VAL* 1.3 67.3 + - - +
25K GLN* 3.4 20.3 + - - +
118K GLY 3.5 27.1 + - - +
119K THR* 4.2 7.0 - - + -
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Residues in contact with VAL 22 (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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12K VAL* 4.0 13.5 - - + -
14K ALA* 5.3 3.6 - - + -
17K CYS* 3.8 18.2 - - + -
18K ILE 3.0 14.7 + - - +
19K MET* 3.5 6.1 - - - +
21K ARG* 1.3 74.7 - - - +
23K ALA* 1.3 56.3 + - - +
25K GLN* 2.8 5.5 + - - +
26K VAL* 2.7 52.0 + - + +
38K VAL* 5.0 3.8 - - + -
79K PHE* 3.9 19.3 - - + -
116K LEU* 3.9 14.6 - - + -
119K THR* 3.7 26.7 - - + +
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Residues in contact with ALA 23 (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 MET 2.7 20.4 + - - +
20K GLY 3.6 4.5 - - - +
22K VAL* 1.3 74.0 - - - +
24K SER* 1.3 56.7 + - - +
26K VAL* 3.1 4.5 + - - +
27K ALA* 2.8 32.4 + - - +
79K PHE* 4.1 5.8 - - + -
82K THR* 3.9 17.9 - - + -
83K ILE* 3.8 29.3 - - + +
86K MET* 3.6 14.0 - - - +
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Residues in contact with SER 24 (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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1102A C 2.5 38.2 + - - +
1103A C 2.8 19.4 + - - +
1109A U 3.1 22.7 - - - -
1247A A 4.1 0.2 - - - -
20K GLY 2.9 13.5 + - - -
21K ARG 3.8 0.2 - - - -
22K VAL 3.2 0.2 - - - -
23K ALA* 1.3 75.1 - - - +
25K GLN* 1.3 59.9 + - - +
27K ALA* 3.6 3.1 + - - +
28K GLU* 3.2 22.0 + - - +
86K MET* 3.3 16.3 - - - -
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Residues in contact with GLN 25 (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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1109A U 4.3 20.4 - - + -
21K ARG* 3.4 8.2 + - - +
22K VAL 2.8 7.6 + - - +
24K SER* 1.3 75.6 - - - +
26K VAL* 1.3 67.2 + - - +
27K ALA 3.1 2.0 - - - -
28K GLU* 3.3 7.7 + - + +
29K GLN* 3.0 38.6 + - - +
116K LEU* 3.9 30.4 - - + +
117K ASP* 3.4 26.5 + - - +
119K THR* 3.4 16.3 - - - +
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Residues in contact with VAL 26 (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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12K VAL* 4.7 2.5 - - + -
22K VAL* 2.7 41.6 + - + +
23K ALA* 3.8 7.0 - - - +
25K GLN* 1.3 73.8 - - - +
27K ALA* 1.3 61.7 + - - +
29K GLN* 3.9 6.3 - - - +
30K ALA* 3.0 22.9 + - - +
36K VAL* 3.5 34.9 - - + +
38K VAL* 4.2 13.9 - - + -
83K ILE* 4.4 10.8 - - + -
101K VAL* 4.0 21.5 - - + -
116K LEU* 4.5 9.2 - - + -
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Residues in contact with ALA 27 (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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1103A C 3.5 22.4 - - - +
23K ALA 2.8 17.1 + - - +
24K SER 3.6 3.4 - - - +
26K VAL* 1.3 73.8 - - - +
28K GLU* 1.3 66.1 + - - +
30K ALA* 3.1 5.7 + - - +
31K LEU* 3.1 28.0 + - - +
83K ILE* 4.6 8.2 - - + +
86K MET* 3.9 12.8 - - + -
87K LEU* 3.8 20.9 - - + +
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Residues in contact with GLU 28 (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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1103A C 3.8 35.4 + - - +
1104A C 4.0 13.6 + - - -
1106A A 5.0 4.9 + - - -
24K SER 3.2 15.2 + - - +
25K GLN* 3.6 9.0 - - + +
27K ALA* 1.3 80.9 - - - +
29K GLN* 1.3 64.5 + - + +
31K LEU* 3.4 6.7 + - - +
32K ASP* 3.0 36.4 + - - +
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Residues in contact with GLN 29 (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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10K VAL* 3.8 28.6 - - - +
25K GLN* 3.0 32.0 + - + +
26K VAL* 3.9 5.7 - - - +
28K GLU* 1.3 78.7 - - + +
30K ALA* 1.3 61.3 + - - +
32K ASP* 2.9 24.1 + - - +
33K GLY 3.3 0.3 + - - -
34K GLU* 3.1 33.7 + - + +
36K VAL* 4.5 8.7 - - + +
116K LEU* 4.2 23.0 - - - +
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Residues in contact with ALA 30 (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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26K VAL 3.0 18.2 + - - +
27K ALA* 3.1 5.8 + - - +
29K GLN* 1.3 77.8 - - - +
31K LEU* 1.3 61.0 + - - +
32K ASP 3.0 0.7 - - - -
33K GLY* 3.2 13.9 + - - -
34K GLU 3.5 14.8 + - - +
36K VAL* 4.6 0.8 - - + +
87K LEU* 5.2 2.2 - - + -
97K ALA* 3.3 30.9 - - + +
100K SER* 4.4 1.4 + - - -
101K VAL* 3.6 26.9 - - + -
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Residues in contact with LEU 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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1103A C 4.6 1.1 - - - +
1104A C 3.4 37.7 - - - +
27K ALA 3.1 12.5 + - - +
28K GLU* 3.7 7.2 - - - +
29K GLN 3.2 0.2 - - - -
30K ALA* 1.3 74.7 - - - +
32K ASP* 1.3 59.6 + - - +
33K GLY 3.2 3.5 + - - -
87K LEU* 3.5 27.8 - - + -
88K PRO* 4.6 5.2 - - + -
93K ARG* 4.3 48.2 + - + +
94K GLY* 4.5 6.7 - - - -
97K ALA* 3.7 17.0 - - + -
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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