Contacts of the helix formed by residues 35 - 45 (chain B) in PDB entry 1P7G
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 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLU* 3.7 10.1 - - - -
32B PRO 6.2 0.2 - - - -
34B ILE* 1.3 77.0 - - - +
36B ALA* 1.3 64.9 + - - +
37B GLU* 3.7 7.3 + - - +
38B ILE* 3.3 31.0 + - - +
39B MSE 3.1 20.1 + - - +
184B LEU* 5.0 2.3 - - - +
185B GLN* 2.8 24.5 + - - +
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Residues in contact with ALA 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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27B TYR* 2.9 35.5 - - + +
28B ASN* 3.8 9.4 - - + -
31B GLU* 3.0 19.8 + - - +
34B ILE 3.7 0.2 + - - -
35B SER* 1.3 71.0 - - - +
37B GLU* 1.3 60.7 + - - +
39B MSE 3.6 1.4 - - - +
40B GLN* 2.8 33.1 + - - +
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Residues in contact with GLU 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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35B SER* 3.3 8.0 + - - +
36B ALA* 1.3 77.0 - - - +
38B ILE* 1.3 63.9 + - - +
40B GLN* 3.4 17.3 + - - +
41B LEU* 3.0 32.3 + - + +
184B LEU* 3.3 32.8 - - + +
187D LYS* 3.3 25.1 + - - -
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.7 18.6 - - + -
35B SER* 3.3 26.8 + - - +
37B GLU* 1.3 79.8 - - - +
39B MSE 1.3 59.0 + - - +
40B GLN 3.2 0.2 + - - -
41B LEU* 3.8 3.5 - - - +
42B HIS* 2.8 39.5 + - + +
180B HIS 4.0 15.8 - - - +
181B ALA* 3.7 15.5 - - - +
182B TYR* 3.9 26.2 - - - -
184B LEU* 3.9 21.5 - - + +
185B GLN* 3.9 26.5 - - + +
186B TYR* 5.5 0.9 - - + -
183D TYR* 6.1 0.2 - - + -
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Residues in contact with MSE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 4.0 11.5 - - + +
25B TYR* 3.8 26.5 - - + +
26B ALA 5.6 0.7 - - - +
27B TYR* 3.4 33.7 - - + +
30B LEU* 4.0 17.9 - - + -
34B ILE* 3.3 32.5 - - + +
35B SER 3.1 15.0 + - - +
36B ALA 3.4 0.9 + - - +
38B ILE* 1.3 81.1 - - - +
40B GLN* 1.3 62.7 + - - +
42B HIS* 4.0 4.9 - - - +
43B HIS* 3.1 26.3 + - - +
93B PHE* 5.7 0.4 - - - -
94B TRP* 3.3 39.6 - - + -
97B MSE 4.6 0.2 - - - -
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Residues in contact with GLN 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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27B TYR* 3.7 24.4 - - + -
36B ALA 2.8 15.9 + - - +
37B GLU* 3.4 21.7 + - - +
39B MSE 1.3 74.3 - - - +
41B LEU* 1.3 67.4 + - + +
43B HIS 3.2 1.2 + - - -
44B GLN* 2.8 59.0 + - - +
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Residues in contact with LEU 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 GLU* 3.0 22.6 + - + +
38B ILE* 3.8 3.4 - - - +
40B GLN* 1.3 86.1 - - + +
42B HIS* 1.3 59.9 + - - +
45B LYS* 2.8 44.6 + - + +
46B HIS* 3.2 10.0 + - + -
180B HIS 5.8 0.2 - - - +
184B LEU* 3.7 21.3 - - + -
183D TYR* 3.6 22.4 - - + +
187D LYS* 3.5 29.6 - - + -
188D ASN* 3.7 21.5 - - - +
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Residues in contact with HIS 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 ILE* 2.8 26.7 + - - +
39B MSE 4.0 2.8 - - - +
41B LEU* 1.3 74.2 - - - +
43B HIS* 1.3 57.0 + - - +
46B HIS* 3.8 10.7 - - + -
47B HIS* 3.0 26.6 + - - +
90B HIS* 2.6 34.8 + + - -
93B PHE* 3.9 15.2 - + - -
94B TRP* 3.5 17.8 - + + -
176B ASP* 2.8 21.0 + - - -
180B HIS* 3.3 25.7 + + - +
181B ALA* 3.5 26.2 - - + +
183D TYR* 5.0 0.2 + - - -
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Residues in contact with HIS 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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20B LEU* 3.7 19.2 - - + +
21B PRO 2.8 28.0 + - - -
22B PRO* 4.2 3.6 - - + -
23B LEU* 3.6 32.6 - - + +
27B TYR* 3.1 25.5 + - + -
39B MSE 3.1 18.8 + - - +
40B GLN 3.7 1.1 - - - +
41B LEU 3.1 0.6 - - - -
42B HIS* 1.3 77.4 - - - +
44B GLN* 1.3 66.9 + - - +
45B LYS 3.4 0.2 - - - -
47B HIS* 3.4 11.6 - - - +
48B GLN 3.3 19.8 + - - -
94B TRP* 3.7 29.6 + - + -
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Residues in contact with GLN 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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20B LEU* 4.6 6.7 - - + -
27B TYR* 3.0 40.0 + - - +
40B GLN* 2.8 42.5 + - - +
43B HIS* 1.3 74.1 - - - +
45B LYS* 1.3 67.6 + - + +
48B GLN* 3.0 23.8 - - - +
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Residues in contact with LYS 45 (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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41B LEU* 2.8 34.7 + - + +
44B GLN* 1.3 85.4 - - + +
46B HIS* 1.3 60.5 + - + +
47B HIS 3.7 0.2 - - - -
48B GLN* 3.8 1.0 - - - +
49B GLY* 3.0 24.3 + - - -
188D ASN* 3.3 46.4 - - + +
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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