Contacts of the helix formed by residues 29 - 42 (chain A) in PDB entry 1S3Y
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ALA* 6.1 0.2 - - + -
27A TRP* 3.8 26.5 + - + +
28A LYS* 1.3 102.5 - - - +
30A LYS* 1.3 64.9 + - - +
31A LYS 3.2 2.2 - - - -
32A GLU* 3.2 30.3 + - + -
33A ILE* 3.1 23.6 + - + +
146A ILE* 4.0 16.6 - - + -
192A GLU* 3.3 10.3 - - - +
195A PHE* 3.8 29.2 - - + -
197A TYR* 3.5 32.1 - - + -
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Residues in contact with LYS 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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28A LYS* 4.0 3.7 - - + +
29A LEU* 1.3 73.4 - - - +
31A LYS* 1.3 86.9 + - - +
33A ILE* 3.7 10.3 + - + +
34A SER* 3.3 18.9 + - - -
192A GLU* 3.0 12.9 + - - +
193A ASP* 4.8 2.8 + - - +
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Residues in contact with LYS 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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30A LYS* 1.3 96.6 - - - +
32A GLU* 1.3 62.1 + - - +
34A SER* 3.1 13.4 + - - -
35A TYR* 3.0 21.3 + - - +
190A ILE* 4.9 10.3 - - + -
192A GLU* 2.9 23.8 + - + +
197A TYR* 3.1 12.3 - - - +
199A PHE* 5.2 3.3 - - + -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 4.2 5.6 - - + +
29A LEU* 3.2 35.3 + - + -
31A LYS* 1.3 78.8 - - - +
33A ILE* 1.3 51.5 + - + +
35A TYR* 2.9 18.3 + - - +
36A PHE 2.8 30.5 + - - -
144A THR* 2.6 43.9 + - + -
197A TYR* 3.7 12.7 + - + +
199A PHE* 4.3 1.7 - - + -
208A TQT 2.7 48.8 + - - +
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Residues in contact with ILE 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* 3.1 21.1 - - + +
30A LYS* 3.7 9.4 - - + +
32A GLU* 1.3 77.6 - - + +
34A SER* 1.3 57.8 + - - +
36A PHE* 3.1 12.0 + - + +
37A LYS* 2.8 40.1 + - + +
208A TQT 3.5 59.0 - - + -
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Residues in contact with SER 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 LYS 3.3 11.6 + - - -
31A LYS* 3.1 21.4 + - - +
32A GLU 3.1 0.4 - - - -
33A ILE* 1.3 80.6 - - - +
35A TYR* 1.3 61.7 + - - +
37A LYS* 3.5 7.0 + - - +
38A ARG* 3.0 36.6 + - - +
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Residues in contact with TYR 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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10A ILE* 5.0 8.5 - - + -
31A LYS 3.0 10.6 + - - +
32A GLU* 2.9 17.2 + - - +
34A SER* 1.3 77.2 + - - +
36A PHE* 1.3 55.7 + - - +
38A ARG* 3.1 13.1 + - - +
39A VAL* 2.8 60.5 + - + +
142A MET* 3.8 27.3 - - + +
143A ALA 5.7 2.2 - - - -
144A THR* 4.5 4.5 - - - -
177A LEU* 3.9 14.8 - - + +
181A VAL* 4.4 0.4 - - + +
185A VAL* 3.5 39.5 - - + -
186A PRO* 5.6 0.9 - - + -
199A PHE* 3.9 47.1 - + + +
200A GLU 5.4 1.4 + - - -
208A TQT 5.0 2.2 - - - -
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Residues in contact with PHE 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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10A ILE* 3.8 18.6 - - + -
32A GLU 2.8 11.5 + - - +
33A ILE* 3.3 17.0 - - + +
35A TYR* 1.3 78.5 - - - +
37A LYS* 1.3 65.5 + - + +
39A VAL* 3.4 0.7 + - - +
40A THR* 2.9 41.3 + - + +
55A VAL* 5.2 0.2 - - + -
72A LEU* 4.3 14.1 - - + -
75A ARG* 4.2 13.5 - - - -
123A ILE* 3.8 42.2 - - + -
208A TQT 3.7 70.9 - + + +
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Residues in contact with LYS 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 ILE* 2.8 27.6 + - + +
34A SER* 3.8 6.3 - - - +
36A PHE* 1.3 75.9 - - + +
38A ARG* 1.3 62.4 + - - +
40A THR* 3.6 0.3 + - - -
41A SER* 2.8 40.0 + - - +
69A PHE* 5.2 13.5 - - - -
75A ARG* 3.8 26.9 - - - +
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Residues in contact with ARG 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 SER* 3.0 28.8 + - - +
35A TYR* 3.1 14.6 + - - +
37A LYS* 1.3 78.5 - - - +
39A VAL* 1.3 63.3 + - - +
41A SER* 4.1 2.2 - - - -
42A PHE* 3.0 27.1 + - + +
181A VAL* 5.1 6.5 - - + -
183A THR* 3.5 40.0 + - + +
184A LYS 4.7 8.3 + - - -
185A VAL* 5.5 1.1 - - - -
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Residues in contact with VAL 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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10A ILE* 4.2 13.2 - - + -
35A TYR* 2.8 64.0 + - + +
36A PHE 3.9 2.7 - - - +
38A ARG* 1.3 75.3 - - + +
40A THR* 1.3 61.1 + - - +
41A SER 3.2 1.3 + - - -
42A PHE* 3.6 11.3 + - - +
53A ASN* 4.5 0.9 + - - -
119A ARG* 5.4 2.1 + - - +
121A PHE* 3.7 26.9 - - + -
142A MET* 3.9 22.9 - - + -
180A TRP* 4.5 2.9 - - + -
181A VAL* 4.0 21.5 - - + -
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Residues in contact with THR 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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10A ILE* 4.0 14.4 - - + -
36A PHE* 2.9 38.2 + - + +
39A VAL* 1.3 74.6 - - - +
41A SER* 1.3 56.7 + - - +
53A ASN* 3.0 21.1 + - - +
55A VAL* 4.1 9.1 - - + +
75A ARG* 2.7 49.4 + - - +
121A PHE* 3.7 33.6 - - + -
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Residues in contact with SER 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 LYS* 2.8 28.7 + - - +
38A ARG* 4.1 2.9 - - - -
40A THR* 1.3 76.4 - - - +
42A PHE* 1.3 69.7 + - - +
43A VAL* 3.4 9.2 + - - +
53A ASN* 3.4 6.7 + - - +
73A LYS 4.7 2.6 + - - -
74A GLY* 5.3 5.3 - - - +
75A ARG* 3.4 27.8 + - - +
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Residues in contact with PHE 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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38A ARG* 3.0 20.6 + - + +
39A VAL* 3.6 9.9 + - - +
41A SER* 1.3 75.8 - - - +
43A VAL* 1.3 81.8 + - - +
44A PRO* 4.6 12.6 - - + -
45A THR* 5.6 6.3 - - + -
53A ASN* 2.7 24.4 + - - +
118A ASN* 3.8 3.3 - - - +
119A ARG* 4.1 17.1 + - - -
179A SER 5.3 0.2 - - - -
180A TRP 4.0 11.0 - - - -
181A VAL* 3.4 29.8 - - + +
182A GLY* 3.6 22.4 - - - -
183A THR* 4.4 15.9 - - + -
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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