Contacts of the helix formed by residues 35 - 44 (chain B) in PDB entry 3P05
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 GLU 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 2.9 52.8 - - - +
33B SER* 2.5 35.3 + - - -
34B PRO* 1.3 73.2 - - - +
36B VAL* 1.3 63.9 + - - +
37B ILE 3.1 1.5 + - - -
38B PRO* 3.4 5.9 - - - +
39B MET* 3.2 20.6 + - - +
173B ARG* 3.8 12.9 + - - +
57C ASN 3.8 8.3 - - - +
58C THR* 3.5 16.3 - - - +
59C VAL 3.7 12.1 - - - +
60C GLY* 3.5 20.5 - - - -
61C GLY 4.8 0.2 + - - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TRP* 4.3 23.2 - - + -
26B VAL* 4.6 9.9 - - + +
27B VAL* 4.4 7.6 - - + -
30B LYS* 4.0 23.8 - - + -
31B ALA 3.3 25.1 - - - +
32B PHE* 4.7 15.0 - - + -
33B SER 3.0 16.7 + - - +
35B GLU* 1.3 79.9 - - - +
37B ILE* 1.3 58.7 + - + +
39B MET* 3.4 6.9 - - - +
40B PHE* 2.8 27.1 + - + +
138B LEU* 5.2 7.0 - - + -
142B VAL* 5.6 1.6 - - + -
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO* 3.3 9.6 + - + +
35B GLU 3.1 1.2 - - - -
36B VAL* 1.3 75.0 - - + +
38B PRO* 1.3 74.9 - - + +
40B PHE* 3.1 8.6 + - - +
41B SER* 3.0 21.9 + - - +
135B ILE* 4.2 28.0 - - + +
138B LEU* 4.0 20.0 - - + -
139B ASN* 2.9 47.8 - - - +
142B VAL* 4.2 17.5 - - + -
176B GLN* 5.4 0.7 - - - +
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Residues in contact with PRO 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PRO 3.5 8.1 - - - +
35B GLU 3.4 9.2 - - - +
37B ILE* 1.3 96.0 - - + +
39B MET* 1.3 55.3 + - - +
41B SER* 3.2 8.5 + - - +
42B ALA* 2.9 30.1 + - - +
173B ARG* 4.1 6.5 - - - +
54C THR* 5.0 4.0 - - + +
57C ASN* 3.3 40.2 - - + +
58C THR* 4.1 12.0 - - + +
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Residues in contact with MET 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B CYS* 5.0 3.4 - - - -
23B TRP* 5.2 1.3 - - + -
26B VAL* 3.9 28.3 - - + -
30B LYS* 3.6 16.4 - - - +
35B GLU 3.2 9.9 + - - +
36B VAL* 3.4 13.0 - - - +
37B ILE 3.2 0.2 - - - -
38B PRO* 1.3 76.2 - - - +
40B PHE* 1.3 66.6 + - - +
42B ALA* 3.2 3.1 + - - +
43B LEU* 2.9 47.8 + - + +
20C LEU* 4.0 27.6 - - - +
21C CYS* 5.8 0.4 - - - -
24C VAL* 3.2 38.6 - - + -
58C THR* 3.7 15.4 - - - +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TRP* 3.8 32.7 - + + -
36B VAL 2.8 20.7 + - - +
37B ILE 3.1 4.7 + - - +
39B MET* 1.3 73.7 - - - +
41B SER* 1.3 65.0 + - - +
43B LEU* 3.4 2.5 + - - +
44B SER* 3.0 27.2 + - - -
52B LEU* 3.7 26.7 - - + -
55B MET* 3.8 21.8 - - + -
56B LEU* 4.7 11.4 - - + -
131B LYS* 3.9 20.6 - - + -
134B ILE* 3.5 33.2 - - + -
135B ILE* 4.0 21.8 - - + -
138B LEU* 4.1 14.8 - - + -
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.0 13.9 + - - +
38B PRO* 3.6 11.3 - - - +
39B MET 3.2 0.2 - - - -
40B PHE* 1.3 78.1 - - - +
42B ALA* 1.3 60.9 + - - +
44B SER* 3.2 18.4 + - - -
45B GLU* 3.4 19.4 + - - +
131B LYS* 3.5 11.9 + - - +
135B ILE* 3.6 24.4 - - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO 2.9 16.6 + - - +
39B MET 3.8 1.6 - - - +
41B SER* 1.3 77.6 - - - +
43B LEU* 1.3 63.7 + - - +
44B SER 3.3 0.7 + - - -
45B GLU* 4.0 18.2 + - - +
15C ILE* 4.8 14.4 - - + +
17C PRO* 5.8 1.7 - - - +
20C LEU* 3.5 30.3 - - + -
54C THR* 3.9 15.3 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 3.7 26.0 - - + +
22B CYS* 4.2 12.1 - - - -
23B TRP* 3.5 44.9 - - + +
39B MET* 2.9 37.9 + - + +
40B PHE 4.0 3.4 - - - +
41B SER 3.3 0.2 - - - -
42B ALA* 1.3 77.0 - - - +
44B SER* 1.3 58.3 + - - +
45B GLU 3.5 1.3 + - - -
55B MET* 4.1 13.8 - - + +
17C PRO* 4.0 35.6 - - + +
20C LEU* 4.9 9.0 - - + -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 3.0 20.2 + - - -
41B SER* 3.2 1.8 + - - -
43B LEU* 1.3 79.5 - - - +
45B GLU* 1.3 65.9 + - - +
46B GLY 3.2 0.2 + - - -
47B ALA* 3.1 22.3 + - - +
52B LEU* 3.9 23.1 - - - -
55B MET* 4.1 12.6 - - - -
131B LYS* 2.8 45.1 + - - +
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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