Contacts of the helix formed by residues 21 - 37 (chain B) in PDB entry 1K7E
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 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.7 17.7 - - + -
18B PRO* 2.9 31.2 + - + +
20B ILE* 1.3 74.6 - - + +
22B MET* 1.4 64.8 + - - +
23B PRO* 3.3 3.8 - - - -
24B ALA* 3.0 20.9 + - + +
25B LEU* 3.4 11.3 + - + +
174B LEU* 4.2 28.5 - - + +
177B TRP* 3.5 35.7 - - + +
178B SER* 3.7 38.6 - - - -
181B TYR* 4.8 2.0 - - + -
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 3.7 35.2 - - + -
134A GLU* 3.8 37.5 - - + +
3B THR* 5.8 0.9 - - + -
15B MET* 3.4 44.4 - - + +
17B VAL* 3.8 17.9 - - + -
19B GLN* 3.1 15.2 + - - +
21B LEU* 1.4 75.8 - - - +
23B PRO* 1.4 63.8 - - + +
25B LEU* 2.8 5.4 + - - +
26B ASN* 2.7 49.3 + - - +
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Residues in contact with PRO 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PRO* 6.4 1.3 - - + -
157A ASN* 3.7 27.1 - - - +
19B GLN* 3.7 6.5 - - - +
20B ILE* 3.4 13.0 - - - +
21B LEU 3.3 4.5 - - - -
22B MET* 1.4 92.8 - - + +
24B ALA* 1.3 56.2 + - - +
26B ASN* 3.9 9.3 - - + +
27B GLN* 2.8 31.8 + - - +
181B TYR* 5.3 9.0 - - + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE 5.1 0.2 + - - -
21B LEU* 3.0 15.6 + - + +
22B MET 3.0 0.8 - - - -
23B PRO* 1.3 83.2 - - - +
25B LEU* 1.3 56.6 + - - +
27B GLN* 3.5 13.5 + - - +
28B LEU* 3.0 27.2 + - - +
103B LYS* 5.7 0.8 + - - +
177B TRP* 3.9 28.2 - - + -
181B TYR* 3.9 29.9 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 3.3 33.8 - - + +
17B VAL* 3.7 29.2 - - + -
21B LEU* 3.4 8.0 + - + +
22B MET* 2.8 5.5 + - - +
24B ALA* 1.3 76.1 - - - +
26B ASN* 1.3 68.8 + - - +
28B LEU* 3.8 4.7 - - + +
29B GLU* 2.9 25.5 + - - +
177B TRP* 3.7 30.1 - - + -
194B PRO* 3.8 20.6 - - + -
195B HIS 3.6 16.8 - - - +
196B PRO* 3.9 5.5 - - + +
197B TYR* 4.0 15.9 - - + -
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 4.8 4.9 - - - +
2B THR 3.7 22.8 + - - +
3B THR* 4.1 6.9 - - - +
15B MET* 3.8 19.2 - - - +
22B MET* 2.7 31.3 + - - +
23B PRO* 3.9 7.6 - - + +
25B LEU* 1.3 80.5 - - - +
27B GLN* 1.3 65.3 + - - +
29B GLU* 3.6 9.3 + - - +
30B GLU* 3.1 22.6 + - - +
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO 2.8 18.7 + - - +
24B ALA* 3.8 10.3 - - - +
26B ASN* 1.3 77.5 - - - +
28B LEU* 1.3 54.7 + - - +
30B GLU* 3.2 7.4 + - + +
31B ALA* 2.6 35.9 + - + +
101B MET* 3.8 29.6 + - + +
103B LYS* 3.0 33.3 + - - +
181B TYR* 4.5 3.8 - - - +
182B GLU* 5.7 0.3 - - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 3.0 17.8 + - - +
25B LEU* 3.8 4.0 - - + +
26B ASN 3.1 0.2 - - - -
27B GLN* 1.3 77.5 - - - +
29B GLU* 1.3 58.7 + - - +
31B ALA* 3.1 1.6 + - - -
32B PHE* 2.8 27.0 + - - +
97B LEU* 4.1 21.8 - - + -
101B MET* 4.0 22.0 - - + -
177B TRP* 4.7 6.3 - - + -
185B HIS* 3.8 20.9 - - + +
196B PRO* 3.9 10.1 - - + -
197B TYR* 3.4 46.9 - - + +
200B ILE* 3.9 11.9 - - + -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B THR* 3.4 11.6 - - - +
4B LEU* 2.8 32.5 + - - +
5B LEU* 2.8 28.9 + - + +
15B MET* 6.4 0.2 - - + -
25B LEU 2.9 17.3 + - - +
26B ASN* 3.6 9.6 + - - +
28B LEU* 1.3 78.9 - - - +
30B GLU* 1.3 57.9 + - - +
32B PHE* 3.1 5.6 + - + +
33B VAL* 2.8 36.2 + - + +
195B HIS* 2.7 32.6 + - + +
196B PRO* 3.8 17.7 - - + +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 3.9 28.9 - - + +
26B ASN 3.1 13.9 + - - +
27B GLN* 3.4 7.4 - - + +
29B GLU* 1.3 77.1 - - - +
31B ALA* 1.3 70.6 + - + +
33B VAL* 3.2 1.9 + - - +
34B SER* 3.0 29.2 + - - -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLN* 2.6 21.5 + - + +
28B LEU 3.1 1.5 + - - +
30B GLU* 1.3 76.4 - - + +
32B PHE* 1.3 64.1 + - - +
34B SER* 3.3 6.6 + - - -
35B ALA* 2.9 24.3 + - - +
97B LEU* 3.9 6.0 - - + +
100B ARG* 3.8 14.8 + - + +
101B MET* 3.8 29.6 - - + -
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.4 17.0 - - + -
28B LEU 2.8 16.5 + - - +
29B GLU* 3.5 7.4 - - - +
30B GLU 3.0 0.2 - - - -
31B ALA* 1.3 79.6 - - - +
33B VAL* 1.3 68.0 + - - +
35B ALA* 3.0 2.0 + - + -
36B GLN* 2.9 64.3 + - + +
97B LEU* 3.9 13.4 - - + +
196B PRO* 5.4 1.1 - - + -
199B THR* 4.0 17.3 - - + -
200B ILE* 3.4 46.4 - - + -
203B GLU* 3.8 23.8 - - + -
204B PHE* 4.0 20.2 - + - -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.8 32.3 - - + -
5B LEU* 4.0 30.3 - - + -
29B GLU* 2.8 20.5 + - + +
30B GLU* 3.2 4.9 + - - +
32B PHE* 1.3 81.5 - - + +
34B SER* 1.3 64.3 - - - +
36B GLN* 3.3 11.1 + - - +
37B LYS* 3.4 39.0 + - + +
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Residues in contact with SER 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 3.0 22.9 + - - -
31B ALA* 3.5 7.0 - - - -
33B VAL* 1.3 78.6 - - - +
35B ALA* 1.3 64.4 + - - +
37B LYS* 2.9 18.5 + - - +
38B ASP* 3.1 12.0 + - - +
100B ARG* 2.8 27.4 + - - -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 2.9 16.9 + - - +
32B PHE* 3.7 3.4 - - + +
34B SER* 1.3 80.5 - - - +
36B GLN* 1.3 59.6 + - - +
38B ASP* 2.8 21.7 + - - +
41B PHE* 3.5 41.8 - - + +
42B GLN* 3.2 10.7 + - - -
97B LEU* 3.8 9.9 - - + -
100B ARG* 3.8 13.5 - - - +
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Residues in contact with GLN 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 2.9 56.5 + - + +
33B VAL* 3.8 7.0 - - - +
35B ALA* 1.3 78.7 - - - +
37B LYS* 1.3 63.4 + - + +
41B PHE* 4.4 1.6 - - - -
42B GLN* 3.2 36.9 + - - +
203B GLU* 4.1 19.6 + - - +
204B PHE* 3.4 22.3 - - - -
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Residues in contact with LYS 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.4 33.5 + - + +
34B SER* 2.9 10.3 + - - +
36B GLN* 1.3 79.7 - - + +
38B ASP* 1.3 59.5 + - - +
39B PRO* 3.3 11.9 - - - +
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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