Contacts of the helix formed by residues 27 - 39 (chain A) in PDB entry 3P9K
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 SER 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A SER* 3.2 1.6 - - - -
26A SER* 1.3 77.4 - - - +
28A VAL* 1.3 68.7 + - - +
29A LEU 3.3 0.2 - - - -
30A PRO* 3.1 21.9 - - - +
31A MET* 3.1 17.2 + - - +
30B PRO* 3.7 8.0 - - - +
31B MET* 5.4 0.4 - - - -
128B ASN* 4.2 6.1 + - - +
129B GLN* 2.8 28.8 + - - -
134B MET* 3.9 32.6 - - - -
137B TRP* 4.6 7.3 + - - -
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Residues in contact with VAL 28 (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 SER* 3.3 17.7 - - - +
26A SER 3.1 0.4 - - - -
27A SER* 1.3 80.0 + - - +
29A LEU* 1.3 57.1 + - - +
31A MET* 4.0 0.5 - - - +
32A THR* 2.8 47.4 + - - +
80A LEU* 3.9 26.2 - - + -
137B TRP* 4.2 15.9 - - + -
312B HIS* 3.8 18.8 - - + +
315B MET* 3.9 12.3 - - + -
316B ILE* 3.7 32.3 - - + -
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Residues in contact with LEU 29 (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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26A SER 3.9 5.0 + - - +
28A VAL* 1.3 81.1 - - - +
30A PRO* 1.3 64.6 - - + +
32A THR* 4.0 0.5 - - - -
33A LEU* 2.9 36.1 + - + +
80A LEU* 4.4 5.4 - - + -
81A LEU* 4.0 21.1 - - + -
84A TYR* 3.7 56.5 - - + -
86A VAL* 4.5 7.4 - - + -
23B LEU* 4.1 20.9 - - + -
26B SER* 4.4 15.5 - - - +
312B HIS* 5.4 2.3 - - + +
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Residues in contact with PRO 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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26A SER 3.2 12.6 - - - +
27A SER* 3.1 24.2 - - - +
29A LEU* 1.3 97.0 - - + +
31A MET* 1.3 58.6 + - + +
33A LEU* 3.8 4.5 - - + +
34A LYS* 3.0 28.8 + - - +
129A GLN* 4.0 19.0 - - + +
23B LEU 5.3 0.7 - - - +
26B SER* 3.3 36.6 - - - +
27B SER* 3.8 19.3 - - - +
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Residues in contact with MET 31 (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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27A SER* 3.1 17.5 + - - +
28A VAL 4.2 0.2 - - - +
30A PRO* 1.3 81.0 - - - +
32A THR* 1.3 65.1 + - - +
34A LYS* 3.4 9.6 + - + +
35A ASN* 2.9 31.6 + - - -
129A GLN* 4.0 25.4 - - - +
134A MET* 4.9 5.2 - - + -
27B SER* 5.6 0.2 - - - -
134B MET* 3.9 25.1 - - + -
137B TRP* 3.4 54.5 - - + +
138B TYR* 4.0 30.3 - - + +
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Residues in contact with THR 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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28A VAL* 2.8 32.8 + - - +
29A LEU 4.0 1.8 - - - -
31A MET* 1.3 75.0 - - - +
33A LEU* 1.3 59.9 - - - +
35A ASN* 3.3 3.3 + - - +
36A ALA* 2.9 27.4 + - - +
77A ILE* 3.6 42.6 - - + +
80A LEU* 4.1 10.5 - - + -
81A LEU* 4.0 10.1 - - + -
137B TRP* 3.8 3.5 - - - -
140B LEU* 4.7 9.2 - - - -
315B MET* 3.5 22.2 - - + +
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Residues in contact with LEU 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 LEU* 2.9 20.6 + - + +
30A PRO* 3.8 4.5 - - + +
32A THR* 1.3 78.6 - - - +
34A LYS* 1.3 63.1 + - - +
36A ALA* 3.1 2.7 + - + +
37A ILE* 2.9 50.0 + - + +
42A LEU* 4.2 16.4 - - + -
81A LEU* 4.1 16.8 - - + +
86A VAL* 4.3 13.7 - - + -
112A LEU* 4.3 13.0 - - + -
125A ALA* 5.2 5.8 - - + -
23B LEU* 3.8 47.6 - - + +
24B ALA 4.9 0.7 - - - +
26B SER* 5.1 1.6 - - - +
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Residues in contact with LYS 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 PRO 3.0 19.7 + - - +
31A MET* 3.7 14.4 - - + +
32A THR 3.3 0.2 - - - -
33A LEU* 1.3 75.7 - - - +
35A ASN* 1.3 61.6 + - - +
37A ILE* 3.2 11.5 + - - +
38A GLU* 2.9 58.7 + - - +
125A ALA* 4.6 6.5 - - + +
126A LEU* 3.9 23.6 - - + -
129A GLN* 2.7 47.1 + - + +
130A ASP* 3.5 13.9 + - - +
131A LYS 4.3 0.6 - - - +
137B TRP 5.9 0.4 - - - +
138B TYR* 3.9 18.8 - - + +
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Residues in contact with ASN 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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31A MET* 2.9 26.1 + - - +
32A THR 3.8 3.1 - - - +
34A LYS* 1.3 81.8 - - - +
36A ALA* 1.3 60.4 + - - +
38A GLU* 3.6 12.3 + - - +
39A LEU* 2.9 39.5 + - + +
77A ILE* 5.6 1.1 - - + -
137B TRP* 2.7 31.1 + - - +
140B LEU* 3.6 29.1 - - + +
141B LYS* 3.0 33.9 + - - +
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Residues in contact with ALA 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 THR 2.9 16.8 + - - +
33A LEU* 3.1 5.6 + - + +
35A ASN* 1.3 75.4 - - - +
37A ILE* 1.3 60.8 + - - +
39A LEU* 3.6 0.4 + - - -
40A GLY 3.2 2.4 + - - -
41A LEU* 2.9 55.7 + - + +
42A LEU* 4.0 9.5 + - + -
77A ILE* 4.2 4.4 - - + +
81A LEU* 3.6 26.7 - - + -
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Residues in contact with ILE 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 LEU* 2.9 36.6 + - + +
34A LYS* 3.4 8.3 - - - +
36A ALA* 1.3 77.5 - - - +
38A GLU* 1.3 60.6 + - - +
40A GLY* 2.9 21.9 + - - -
42A LEU* 4.2 15.5 - - + -
43A GLU* 4.9 2.9 - - - +
112A LEU* 4.6 10.8 - - + +
122A ALA* 4.0 29.6 - - + -
125A ALA* 3.7 29.8 - - + -
126A LEU* 4.2 19.3 - - + -
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Residues in contact with GLU 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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34A LYS* 2.9 50.0 + - - +
35A ASN* 3.4 16.3 + - - +
37A ILE* 1.3 77.6 - - - +
39A LEU* 1.3 60.1 + - - +
40A GLY 3.5 0.5 + - - -
126A LEU* 3.4 20.5 - - + +
138B TYR* 6.0 1.2 - - - -
141B LYS* 3.4 41.9 - - + +
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Residues in contact with LEU 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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35A ASN* 2.9 26.4 + - + +
37A ILE 3.2 0.2 - - - -
38A GLU* 1.3 77.0 - - - +
40A GLY* 1.3 58.5 + - - +
41A LEU* 3.9 28.9 - - + -
62A LEU* 3.2 25.0 - - + +
77A ILE* 4.5 6.3 - - + -
140B LEU 5.4 0.2 - - - -
141B LYS* 3.8 26.2 - - + +
144B VAL* 3.9 31.2 - - + -
145B LEU* 3.7 39.7 - - + -
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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