Contacts of the helix formed by residues 22 - 34 (chain A) in PDB entry 3TPZ
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 ASP 22 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.8 2.0 - - + +
21A ASN* 1.3 83.3 + - - +
23A GLN* 1.3 57.7 + - - +
24A PHE* 3.1 26.5 + - - +
25A VAL* 3.4 28.7 + - + +
26A ILE* 2.8 34.3 + - - +
179A SER 5.2 1.0 - - - +
180A ALA* 3.6 20.8 + - + +
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Residues in contact with GLN 23 (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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21A ASN 3.5 6.8 + - - +
22A ASP* 1.3 72.5 + - - +
24A PHE* 1.3 67.4 + - + +
26A ILE* 3.4 16.9 + - - +
27A ASP* 2.9 60.4 + - - +
54A PRO* 6.0 3.4 - - - +
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Residues in contact with PHE 24 (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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22A ASP* 3.1 12.5 + - - +
23A GLN* 1.3 81.7 - - + +
25A VAL* 1.3 64.9 + - + +
27A ASP* 4.0 12.2 - - + +
28A SER* 3.2 21.3 + - - -
31B SER 4.6 0.7 - - - +
34B ASN* 3.5 34.1 + - - +
36B GLN* 4.1 15.3 - - - +
58B ARG* 3.5 36.6 - - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.0 17.0 - - + -
22A ASP* 3.2 30.8 + - + +
24A PHE* 1.3 74.2 - - - +
26A ILE* 1.3 60.8 + - - +
28A SER* 3.1 8.2 + - - -
29A ILE* 2.9 46.6 + - + +
174A LEU* 4.3 12.1 - - + -
175A GLU 6.1 0.9 - - - +
176A VAL* 4.2 15.0 - - + -
177A PRO* 5.5 6.1 - - + -
180A ALA* 4.4 8.3 - - + -
34B ASN* 5.0 8.5 - - - +
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Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.1 38.1 - - + +
21A ASN 4.2 2.2 - - - -
22A ASP 2.8 37.3 + - - +
23A GLN* 3.6 18.2 - - - +
25A VAL* 1.3 75.6 - - - +
27A ASP* 1.3 62.3 + - - +
28A SER 3.2 0.2 + - - -
29A ILE* 3.3 3.9 + - - +
30A VAL* 2.9 33.9 + - + +
50A ALA* 3.5 29.8 - - + +
51A LEU* 3.9 12.3 - - + -
54A PRO* 3.9 17.0 - - + -
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Residues in contact with ASP 27 (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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23A GLN* 2.9 51.0 + - - +
24A PHE* 4.0 14.1 - - + +
26A ILE* 1.3 74.9 - - - +
28A SER* 1.3 57.9 + - - +
30A VAL* 3.9 6.5 - - - +
31A SER* 3.1 29.3 + - - -
54A PRO* 5.3 5.7 - - - +
58A ARG* 5.6 0.2 + - - -
31B SER* 3.5 24.9 + - - +
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Residues in contact with SER 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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24A PHE 3.2 15.7 + - - -
25A VAL* 3.1 13.3 + - - -
27A ASP* 1.3 74.5 - - - +
29A ILE* 1.3 60.1 + - - +
31A SER* 2.9 6.1 + - - -
32A ALA* 2.8 30.2 + - - +
174A LEU* 4.1 20.0 - - - +
31B SER 3.2 13.2 + - - -
32B ALA 3.7 15.9 + - - -
34B ASN* 4.9 7.3 - - - +
193B ARG* 4.1 10.4 + - - -
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Residues in contact with ILE 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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20A LEU* 3.7 18.8 - - + -
25A VAL* 2.9 33.1 + - + +
26A ILE 3.6 5.4 - - - +
28A SER* 1.3 71.7 - - - +
30A VAL* 1.3 56.6 + - - +
32A ALA* 3.2 8.8 + - - +
33A ILE* 2.8 47.5 + - + +
51A LEU* 4.0 19.1 - - + -
139A MET* 3.7 29.8 - - + -
173A VAL* 6.2 0.4 - - - -
174A LEU* 3.9 17.2 - - + +
191A VAL* 4.0 21.1 - - + -
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Residues in contact with VAL 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 ILE* 2.9 25.4 + - + +
27A ASP* 4.0 7.6 - - - +
29A ILE* 1.3 75.7 - - - +
31A SER* 1.3 58.2 + - - +
33A ILE* 3.2 6.2 + - + -
34A ASN 2.8 24.8 + - - -
35A PRO* 3.3 15.6 - - + +
51A LEU* 4.3 10.5 - - + -
54A PRO* 3.9 36.8 - - + +
55A VAL* 4.4 13.9 - - + -
58A ARG* 3.5 29.2 - - - +
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Residues in contact with SER 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 ASP 3.1 9.1 + - - -
28A SER 2.9 14.2 + - - -
30A VAL* 1.3 76.7 - - - +
32A ALA* 1.3 59.5 + - - +
34A ASN* 3.4 8.4 + - - +
58A ARG* 4.1 13.9 - - - +
28B SER* 4.1 14.4 - - - -
31B SER* 3.4 20.9 - - - -
32B ALA* 3.4 25.1 - - - +
173B VAL* 3.3 27.0 - - - +
193B ARG* 5.6 0.2 + - - -
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Residues in contact with ALA 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 SER 2.8 13.7 + - - +
29A ILE* 3.3 13.5 - - - +
31A SER* 1.3 77.3 + - - +
33A ILE* 1.3 63.6 + - + +
34A ASN* 4.3 2.8 - - - +
137A HIS* 3.9 4.6 + - + -
173A VAL* 4.0 28.0 - - + -
191A VAL* 6.0 1.1 - - + -
193A ARG* 2.9 28.1 + - - +
173B VAL* 3.5 15.6 - - + +
193B ARG* 4.2 9.4 - - - +
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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
----------------------------------------------------------
29A ILE* 2.8 40.5 + - + +
30A VAL* 3.2 7.8 + - + +
32A ALA* 1.3 72.8 - - - +
34A ASN* 1.3 64.4 + - - +
35A PRO* 4.1 8.1 - - + -
41A MET* 3.6 30.1 - - + -
51A LEU* 5.2 2.0 - - + -
55A VAL* 4.9 5.6 - - + -
109A ARG* 2.6 35.1 + - + +
111A PHE* 3.7 36.8 - - + -
137A HIS* 3.8 31.9 - - + +
191A VAL* 6.1 0.2 - - + -
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Residues in contact with ASN 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 VAL 2.8 11.9 + - - -
31A SER* 3.5 5.3 - - - +
32A ALA 3.2 2.2 - - - +
33A ILE* 1.3 81.6 - - - +
35A PRO* 1.3 67.1 - - - +
36A GLN* 3.5 28.0 + - - +
39A GLN* 4.1 0.7 + - - +
58A ARG* 3.8 13.6 + - - +
109A ARG* 3.2 7.4 + - - -
24B PHE* 5.2 0.9 - - - -
173B VAL 3.3 27.6 + - - +
174B LEU* 3.4 30.0 - - - +
175B GLU* 4.7 6.3 - - - +
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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