Contacts of the helix formed by residues 35 - 45 (chain M) in PDB entry 6FF7
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 VAL 35 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLN 5.0 0.4 - - - -
33M PHE 4.6 2.2 - - - -
34M SER* 1.3 71.8 - - - +
36M LYS* 1.3 58.9 + - - +
37M CYS 3.3 1.3 - - - -
38M TRP* 3.0 15.3 + - + +
39M LEU* 2.9 27.2 + - - +
63M LEU* 5.0 14.8 - - + -
64M LEU 5.7 2.9 - - - +
67M SER* 3.6 31.3 - - - +
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Residues in contact with LYS 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M SER* 3.3 9.2 - - - -
35M VAL* 1.3 78.1 - - - +
37M CYS* 1.3 58.5 + - - +
39M LEU* 3.2 6.8 + - - +
40M ARG* 2.9 30.7 + - - +
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Residues in contact with CYS 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ASN* 3.6 31.4 - - + +
34M SER* 3.9 8.9 + - - +
35M VAL 3.3 0.6 - - - -
36M LYS* 1.3 80.0 - - - +
38M TRP* 1.3 57.0 + - - +
40M ARG* 4.6 4.0 - - - +
41M TYR* 2.8 34.7 + - - +
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Residues in contact with TRP 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ASN 3.9 3.4 + - - -
32M GLN* 3.3 26.7 - - - +
35M VAL* 3.0 20.2 + - + +
37M CYS* 1.3 77.3 - - - +
39M LEU* 1.3 58.9 + - - +
41M TYR* 4.6 2.2 - - - -
42M ILE* 2.8 30.7 + - - +
59M ARG* 4.3 20.8 - - + +
60M ALA* 6.1 0.7 - - - -
63M LEU* 6.2 0.9 - - + -
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Residues in contact with LEU 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M VAL 2.9 12.6 + - - +
36M LYS* 3.2 9.4 + - - +
38M TRP* 1.3 75.1 - - - +
40M ARG* 1.3 60.0 + - - +
42M ILE* 3.4 4.8 + - - +
43M GLU* 2.9 29.8 + - - +
67M SER* 6.1 2.5 - - - -
70M LEU* 5.2 18.2 - - + +
71M TRP* 6.0 1.3 - - - +
74M TYR* 5.8 6.7 - - + +
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Residues in contact with ARG 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36M LYS 2.9 17.0 + - - +
37M CYS* 4.5 4.0 - - - +
39M LEU* 1.3 75.3 - - - +
41M TYR* 1.3 58.1 + - - +
43M GLU* 3.2 7.9 + - - +
44M PHE* 2.9 29.6 + - - +
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Residues in contact with TYR 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ILE* 3.7 38.1 - - + +
31M ASN* 5.1 3.4 - - + -
37M CYS 2.8 24.4 + - - +
38M TRP* 4.4 2.5 - - - +
40M ARG* 1.3 77.1 - - - +
42M ILE* 1.3 61.7 + - - +
44M PHE* 3.3 15.2 + - - +
45M LYS* 3.4 15.8 + - - +
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Residues in contact with ILE 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M TRP 2.8 23.9 + - - +
39M LEU* 3.7 5.8 - - - +
41M TYR* 1.3 76.3 - - - +
43M GLU* 1.3 60.8 + - - +
44M PHE 3.6 0.3 + - - -
45M LYS* 3.8 15.1 + - - +
52M ARG* 4.2 15.1 - - + +
55M GLN* 6.4 1.6 - - - -
56M LEU* 3.9 29.4 - - + +
74M TYR* 6.4 2.7 - - + -
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Residues in contact with GLU 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M LEU 2.9 17.2 + - - +
40M ARG* 3.2 7.8 + - - +
42M ILE* 1.3 77.7 - - - +
44M PHE* 1.3 59.2 + - - +
45M LYS 3.4 5.1 + - - +
74M TYR* 6.0 5.8 - - + -
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Residues in contact with PHE 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40M ARG 2.9 15.9 + - - +
41M TYR* 3.3 9.4 + - - +
42M ILE 3.3 0.8 - - - -
43M GLU* 1.3 77.7 - - - +
45M LYS* 1.3 58.7 + - - +
46M GLN* 4.1 1.4 + - - +
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Residues in contact with LYS 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU* 5.6 7.4 - - + -
28M ILE* 5.9 4.3 - - + -
41M TYR 3.4 12.7 + - - +
42M ILE* 3.8 14.0 + - - +
43M GLU 3.4 5.1 - - - +
44M PHE* 1.3 79.0 - - - +
46M GLN* 1.3 63.4 + - - +
51M PRO* 3.7 26.9 - - + -
52M ARG* 4.4 12.2 - - - +
55M GLN* 5.9 2.2 - - + -
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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