Contacts of the helix formed by residues 20 - 37 (chain E) in PDB entry 6KW5
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 THR 20 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A ASN 3.5 10.1 - - - -
273A TRP* 3.5 20.4 - - + +
274A TYR 3.3 19.5 - - - +
275A ALA* 5.0 0.4 - - - -
276A LEU* 3.8 6.5 - - - -
18E ASN* 5.4 8.1 - - - +
19E VAL* 1.3 77.8 - - - +
21E LEU* 1.3 60.3 + - - +
22E LYS* 3.4 7.1 + - - +
23E ASN* 2.9 38.9 + - - +
24E LEU* 3.1 30.7 + - - +
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A PRO 4.9 3.4 - - - +
272A ASN* 3.5 35.4 + - - +
274A TYR 4.2 1.8 + - - -
276A LEU* 3.7 17.1 - - + +
20E THR* 1.3 74.2 - - - +
22E LYS* 1.3 57.2 + - - +
24E LEU* 3.6 1.5 + - + +
25E THR* 2.7 42.9 + - - +
443I VAL* 3.7 28.0 - - + -
270J HIS* 4.9 3.6 - - + -
276J LEU* 4.6 4.0 - - + -
279J SER* 4.7 4.3 - - - +
281J PHE* 3.7 30.5 - - + -
282J THR* 3.7 26.2 - - - +
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Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASN* 3.5 17.2 + - + +
273A TRP* 4.3 24.6 - - + +
20E THR* 3.3 7.5 + - - +
21E LEU* 1.3 81.5 - - - +
23E ASN* 1.3 59.2 + - - +
25E THR* 3.9 1.3 - - - -
26E ALA* 2.9 33.5 + - + +
444I LEU* 4.0 24.9 - - + +
447I ASP* 5.9 2.7 + - + +
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Residues in contact with ASN 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ILE* 6.2 1.6 - - + -
313A ARG* 4.4 18.5 + - - +
18E ASN* 4.2 6.1 + - - -
19E VAL* 4.0 12.9 - - + +
20E THR* 2.9 45.2 + - - +
21E LEU 3.3 0.2 - - - -
22E LYS* 1.3 79.3 - - - +
24E LEU* 1.3 57.7 + - - +
26E ALA* 3.5 4.3 + - - +
27E PHE* 2.9 30.7 + - - +
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 3.7 31.4 - - + -
278A THR* 5.8 0.9 - - + -
300A VAL* 4.3 3.8 - - + -
301A VAL* 3.8 26.9 - - + -
309A ILE* 3.7 28.3 - - + -
19E VAL* 4.7 15.5 - - + -
20E THR 3.1 14.7 + - - +
21E LEU* 4.0 3.4 - - - +
23E ASN* 1.3 75.4 - - - +
25E THR* 1.3 58.8 + - - +
27E PHE* 3.4 6.0 + - + +
28E GLN* 3.0 31.0 + - - +
281J PHE* 4.0 37.8 - - + -
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Residues in contact with THR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E LEU* 2.7 31.1 + - - +
22E LYS* 4.0 2.7 - - - -
24E LEU* 1.3 76.1 - - - +
26E ALA* 1.3 57.4 + - - +
28E GLN* 3.5 4.9 + - - +
29E LEU* 2.9 31.9 + - - +
440I ASN* 3.7 44.7 + - + +
443I VAL* 3.7 25.0 - - + +
444I LEU* 3.9 11.9 - - + -
281J PHE* 4.8 8.4 - - - -
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LYS* 2.9 21.5 + - + +
23E ASN* 3.9 5.4 - - - +
25E THR* 1.3 75.2 - - - +
27E PHE* 1.3 59.2 + - - +
29E LEU* 4.0 2.5 - - - +
30E LEU* 2.9 32.7 + - - +
444I LEU* 4.3 21.7 - - + +
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Residues in contact with PHE 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A THR* 4.7 8.7 - - + -
308A LEU* 4.3 25.8 - - + -
309A ILE* 3.6 42.2 - - + -
312A GLU* 3.2 33.7 - - + -
23E ASN 2.9 18.1 + - - +
24E LEU* 3.7 7.0 - - + +
26E ALA* 1.3 76.5 - - - +
28E GLN* 1.3 60.8 + - + +
30E LEU* 3.8 7.5 - - + +
31E SER* 3.0 41.6 + - - -
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Residues in contact with GLN 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU 3.0 15.7 + - - +
25E THR* 4.0 3.1 - - - +
27E PHE* 1.3 82.4 - - + +
29E LEU* 1.3 58.0 + - - +
31E SER* 3.8 3.8 - - - -
32E GLN* 2.9 43.0 + - + +
432I HIS* 5.9 4.2 - - - -
436I SER* 4.6 7.5 + - - -
440I ASN* 4.3 19.8 + - - +
280J PRO* 5.8 1.9 - - - +
281J PHE* 3.2 35.6 - - + -
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E THR 2.9 17.9 + - - +
26E ALA* 4.0 4.0 - - - +
28E GLN* 1.3 75.6 - - - +
30E LEU* 1.3 60.6 + - + +
32E GLN* 3.8 7.9 - - - +
33E ARG* 2.9 80.2 + - + +
437I SER* 4.4 6.7 - - - +
440I ASN* 3.7 39.9 - - + +
441I GLU* 3.8 18.8 - - + +
444I LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 5.2 9.6 - - - +
26E ALA 2.9 19.1 + - - +
27E PHE* 3.8 8.3 - - + +
29E LEU* 1.3 81.8 - - + +
31E SER* 1.3 59.6 + - - +
33E ARG* 3.3 14.7 + - + +
34E GLU* 3.0 65.5 + - + +
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Residues in contact with SER 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 5.9 1.3 - - - -
27E PHE* 3.0 34.3 + - - -
28E GLN* 4.1 3.6 - - - -
30E LEU* 1.3 82.1 - - - +
32E GLN* 1.3 58.3 + - - +
33E ARG 3.5 0.2 - - - -
34E GLU* 4.0 10.1 - - - +
35E ASN* 2.8 37.7 + - - -
415I LYS* 5.3 8.7 - - - +
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Residues in contact with GLN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLN* 2.9 29.6 + - + +
29E LEU* 3.8 5.3 - - - +
30E LEU 3.2 0.2 - - - -
31E SER* 1.3 77.0 - - - +
33E ARG* 1.3 62.6 + - + +
35E ASN* 3.6 15.2 + - - +
36E ILE* 3.6 8.5 + - - +
418I PHE* 5.6 9.5 - - + -
432I HIS* 4.4 10.5 + - - -
433I TYR* 3.4 51.3 + - + +
436I SER* 3.9 17.9 + - - -
437I SER* 4.6 5.9 + - - -
440I ASN* 3.8 20.6 + - - -
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Residues in contact with ARG 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 2.9 48.1 + - + +
30E LEU* 4.1 14.5 - - + +
32E GLN* 1.3 76.7 - - + +
34E GLU* 1.3 62.2 + - - +
35E ASN 3.2 0.7 - - - -
36E ILE* 3.4 11.3 - - - +
37E CYS* 3.2 24.8 - - - -
387H SER 5.1 8.1 - - - +
390H MET* 3.5 43.9 - - + +
433I TYR* 3.8 15.9 - - + +
437I SER* 4.8 10.1 - - - +
441I GLU* 4.7 10.8 + - - +
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Residues in contact with GLU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 5.8 0.2 - - - +
30E LEU* 3.0 50.4 + - + +
31E SER* 4.2 9.4 + - - +
32E GLN 3.4 0.4 - - - -
33E ARG* 1.3 77.4 - - - +
35E ASN* 1.3 63.0 + - - +
37E CYS* 3.8 8.7 + - - +
38E GLU* 3.6 22.1 + - - +
43E VAL* 5.1 3.0 - - - +
48E ARG* 4.1 19.4 + - - -
415I LYS* 4.5 16.7 + - - +
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Residues in contact with ASN 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E SER* 2.8 27.5 + - - +
32E GLN* 3.6 8.9 + - - +
33E ARG 3.2 1.0 - - - -
34E GLU* 1.3 79.4 - - - +
36E ILE* 1.3 62.8 + - - +
37E CYS 3.6 0.3 + - - -
38E GLU* 3.6 7.0 + - - +
39E LEU* 4.3 1.6 + - - +
421H TYR* 5.2 0.5 + - - -
415I LYS* 4.1 27.2 - - - +
418I PHE* 3.6 41.6 - - + +
419I PHE* 3.2 37.9 - - + -
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Residues in contact with ILE 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E GLN 3.6 4.7 + - - +
33E ARG* 3.4 17.0 - - - +
35E ASN* 1.3 77.4 - - - +
37E CYS* 1.3 60.6 + - - +
38E GLU 3.2 6.5 + - - -
39E LEU* 3.4 34.5 + - + +
40E LEU* 3.9 11.9 + - + +
390H MET* 4.1 10.8 - - + -
393H VAL* 4.5 13.5 - - + -
397H VAL* 4.6 9.2 - - + -
418I PHE* 5.0 6.7 - - + -
422I LEU* 5.3 3.8 - - + -
430I LEU* 4.2 22.0 - - + -
433I TYR* 3.3 46.9 - - + +
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Residues in contact with CYS 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG* 3.2 22.6 + - - +
34E GLU* 3.8 5.6 + - - +
35E ASN 3.3 1.0 - - - -
36E ILE* 1.3 78.3 - - - +
38E GLU* 1.3 60.8 + - - +
39E LEU 3.5 0.2 - - - -
40E LEU* 4.8 1.3 - - - +
41E ASN* 3.5 16.7 + - - -
42E LEU* 3.5 39.2 + - + -
43E VAL* 3.4 29.2 - - + +
390H MET* 4.3 21.3 - - - -
393H VAL* 5.3 2.0 - - - -
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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