Contacts of the helix formed by residues 29 - 43 (chain A) in PDB entry 3K9S
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 LYS 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 2.9 26.0 + - + +
27A HIS 3.3 0.2 - - - -
28A THR* 1.3 96.7 + - - +
30A HIS* 1.3 64.5 + - - +
31A HIS 3.5 0.2 - - - -
32A GLN* 3.9 1.2 - - - +
33A THR* 2.9 33.0 + - - +
179B ASN* 3.8 39.5 - - - +
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Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE 3.3 14.2 + - - -
26A HIS* 3.3 25.1 - + + +
29A LYS* 1.3 79.3 - - - +
31A HIS* 1.3 64.1 + - - +
33A THR* 3.1 14.7 + - - -
34A TYR* 3.2 30.9 + - + -
169A TRP* 5.7 0.8 - - - -
171A HIS* 3.2 40.4 + + + +
170B GLU* 3.5 9.2 + - - -
174B TYR* 2.8 31.0 + + - -
179B ASN* 3.5 25.2 - - + +
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Residues in contact with HIS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.4 12.2 - - + +
5A PRO* 3.5 24.3 - - + +
26A HIS* 2.9 16.2 + - - +
27A HIS* 3.4 15.3 - - - +
29A LYS 3.5 0.2 - - - -
30A HIS* 1.3 71.5 - - - +
32A GLN* 1.3 64.5 + - - +
34A TYR* 3.1 20.2 + + - +
35A VAL* 3.1 9.7 + - + +
78A HIS* 3.0 39.2 + - - -
81A HIS* 3.5 12.2 - - + +
82A SER* 3.6 19.7 - - - -
85A TRP* 2.8 33.0 + - + -
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Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.5 32.3 - - + +
27A HIS 3.3 5.9 + - - +
28A THR 3.2 28.3 - - - +
29A LYS* 3.9 1.8 - - - +
30A HIS 3.3 0.4 - - - -
31A HIS* 1.3 78.0 - - - +
33A THR* 1.3 58.5 + - - +
35A VAL* 3.2 15.9 + - - +
36A ASN* 2.9 64.5 + - - +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 2.9 24.3 + - - -
30A HIS* 3.1 6.0 + - - -
32A GLN* 1.3 76.9 - - - +
34A TYR* 1.3 61.7 + - + +
36A ASN* 3.3 10.6 + - + +
37A ASN* 2.9 49.6 + - - +
74A ASN* 5.3 0.4 - - - +
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS* 3.2 29.3 + - + +
31A HIS* 3.1 13.8 + + - +
33A THR* 1.3 78.6 - - + +
35A VAL* 1.3 64.3 + - - +
38A ALA* 2.9 27.5 + - - +
73A ASN 4.5 3.6 - - - -
74A ASN* 3.5 37.4 - - - +
77A GLY* 3.8 21.1 - - - -
78A HIS* 4.0 6.7 - - - +
81A HIS* 3.4 24.4 - + - -
146A GLN* 2.8 23.1 + - + -
169A TRP* 4.3 6.6 - + - -
171A HIS* 3.7 19.6 - - - -
124B PHE* 3.9 24.0 - + - -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 3.5 34.4 - - + +
3A THR* 3.9 6.3 - - - -
4A LEU* 4.0 15.5 - - + +
31A HIS* 3.1 17.8 + - + +
32A GLN* 3.4 19.1 - - - +
34A TYR* 1.3 78.4 - - - +
36A ASN* 1.3 65.6 + - - +
38A ALA* 3.8 3.1 - - - +
39A ASN* 2.9 30.3 + - - +
78A HIS* 3.7 35.0 - - + +
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Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 2.9 52.0 + - - +
33A THR* 3.3 11.3 + - + +
35A VAL* 1.3 78.1 - - - +
37A ASN* 1.3 62.2 + - - +
39A ASN* 3.7 5.9 + - - +
40A ALA* 3.0 29.8 + - - +
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR* 2.9 34.7 + - - +
36A ASN* 1.3 79.4 - - - +
38A ALA* 1.3 62.7 + - - +
40A ALA* 3.4 7.1 + - - +
41A ALA* 3.1 22.9 + - - +
70A VAL* 4.8 6.1 - - + +
74A ASN* 3.3 37.1 + - - +
124B PHE* 6.1 0.8 - - - -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 3.7 30.1 - - + -
34A TYR 2.9 18.8 + - - +
35A VAL 3.8 0.4 - - - +
37A ASN* 1.3 78.5 - - - +
39A ASN* 1.3 58.0 + - - +
41A ALA* 3.1 3.2 + - - +
42A LEU* 2.9 35.0 + - - +
71A LEU* 4.0 16.6 - - + -
74A ASN* 3.8 13.0 - - + +
75A ALA 4.1 5.4 - - - +
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A SER* 3.8 13.4 - - - -
2A TYR* 2.9 54.0 + - - +
35A VAL* 2.9 26.0 + - - +
36A ASN* 3.7 6.5 + - - +
38A ALA* 1.3 75.2 - - - +
40A ALA* 1.3 63.9 + - - +
42A LEU* 3.2 8.0 + - - +
43A GLU* 3.1 24.8 + - - +
49A ALA 5.6 0.5 - - - +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASN 3.0 18.4 + - - +
37A ASN* 3.6 8.3 - - - +
38A ALA 3.2 0.2 - - - -
39A ASN* 1.3 78.7 - - - +
41A ALA* 1.3 61.8 + - - +
43A GLU* 3.5 16.9 + - - +
44A SER* 4.8 0.3 + - - -
67A LYS* 4.7 2.4 + - - -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN 3.1 16.8 + - - +
38A ALA 3.6 4.5 - - - +
40A ALA* 1.3 78.1 - - - +
42A LEU* 1.3 59.6 + - - +
43A GLU 3.6 0.7 + - - -
44A SER* 3.8 1.6 + - - -
45A LEU* 3.8 4.9 - - - +
67A LYS* 2.8 36.2 + - + +
70A VAL* 3.7 32.8 - - + -
71A LEU* 4.1 13.7 - - + -
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 3.7 38.1 - - + +
38A ALA 2.9 20.2 + - - +
39A ASN* 3.2 8.7 + - - +
41A ALA* 1.3 75.0 - - - +
43A GLU* 1.3 63.6 + - - +
44A SER 3.3 2.9 - - - -
45A LEU* 3.0 17.7 + - + +
48A PHE* 3.9 28.0 - - + -
49A ALA* 3.4 39.9 - - + +
56A LEU* 3.9 9.0 - - + -
71A LEU* 3.6 28.0 - - + -
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN 3.1 11.3 + - - +
40A ALA* 3.7 14.8 - - - +
41A ALA 3.4 1.0 - - - -
42A LEU* 1.3 79.5 - - - +
44A SER* 1.3 58.9 + - - +
45A LEU 3.3 2.4 + - - -
46A PRO* 4.3 8.1 - - - +
49A ALA* 5.5 0.6 - - - +
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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