Contacts of the helix formed by residues 34 - 44 (chain C) in PDB entry 5FJV
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 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C GLU* 1.3 90.3 - - - +
35C ARG* 1.3 58.1 + - - +
36C LEU* 4.6 5.8 - - + +
37C PHE* 2.5 55.1 + - + +
38C LYS* 2.9 8.7 + - - +
101C PHE* 5.3 1.0 - - - -
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PRO* 4.7 10.1 - - + +
53B ASN 2.2 35.6 + - - -
54B THR* 2.5 44.5 + - - +
92B TYR* 4.2 8.8 + - - -
33C GLU 4.0 4.1 + - - +
34C ASP* 1.3 71.4 - - - +
36C LEU* 1.3 60.3 + - - +
38C LYS* 3.7 13.4 + - - +
39C HIS* 3.9 13.9 - - - -
102C GLY 6.4 0.2 - - - -
103C ASN* 3.7 25.3 - - + +
107C LEU* 5.6 4.1 - - + +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASN 3.7 24.5 - - - +
46B ARG 5.9 0.4 - - - -
47B TRP* 4.0 25.3 - - + +
50B PRO* 3.9 22.8 - - + +
93B LYS* 4.4 22.0 - - + +
34C ASP* 5.3 4.5 - - + -
35C ARG* 1.3 77.6 - - - +
37C PHE* 1.3 70.0 + - + +
38C LYS 3.3 0.6 + - - -
39C HIS* 3.4 17.4 - - - +
40C LEU* 3.5 20.9 + - + +
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Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 3.2 29.8 - - - -
34C ASP* 2.5 36.5 + - + +
36C LEU* 1.3 84.0 - - + +
38C LYS* 1.3 57.6 + - - -
40C LEU* 3.1 44.5 - - + +
41C PHE* 3.4 10.3 + - + +
101C PHE* 5.2 7.4 - + - -
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP 2.9 6.6 + - - +
35C ARG* 4.0 11.0 - - - +
36C LEU 3.3 0.4 - - - -
37C PHE* 1.3 73.1 - - - +
39C HIS* 1.3 71.3 + - + +
40C LEU 3.0 1.6 - - - -
41C PHE* 2.9 20.2 + - + +
42C ARG* 3.2 11.7 + - + +
96C TRP* 2.6 70.0 - - - +
101C PHE* 3.8 43.3 - - + +
104C ILE 4.1 6.6 + - - +
105C THR* 3.9 12.7 + - - +
106C SER 4.6 0.2 - - - +
107C LEU* 6.4 0.4 - - - +
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TRP* 2.9 42.9 + + + +
49B ARG* 3.7 16.9 - - + +
50B PRO* 4.4 7.5 - - + -
35C ARG 3.9 14.4 - - - -
36C LEU 3.4 9.8 + - - +
38C LYS* 1.3 79.4 - - + +
40C LEU* 1.3 65.6 + - + +
41C PHE 2.9 1.7 + - - -
42C ARG* 3.0 15.8 + - - +
43C GLY* 3.0 14.9 + - - -
107C LEU* 4.3 18.7 - - + +
108C ARG 5.1 0.8 + - - -
109C VAL* 3.3 34.4 - - + +
110C PRO* 4.8 1.3 - - + -
113C MET* 5.7 2.8 - - - -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 3.6 21.1 - - + +
37C PHE* 3.1 43.0 + - + +
39C HIS* 1.3 81.3 - - + +
41C PHE* 1.3 55.3 + - - +
43C GLY 4.5 0.2 - - - -
44C TYR* 3.1 40.4 - - + +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PHE* 3.4 9.9 + - + +
38C LYS* 2.9 17.2 + - + +
40C LEU* 1.3 81.2 - - - +
42C ARG* 1.3 116.4 + - + +
44C TYR* 4.5 4.3 + - - +
45C ASN* 5.1 2.9 + - - +
95C ARG 4.5 2.9 - - - -
96C TRP* 4.6 10.5 - - + -
101C PHE* 4.3 22.9 - + + -
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LYS* 3.2 13.0 + - + +
39C HIS* 3.0 6.9 + - - +
41C PHE* 1.3 134.5 + - + +
43C GLY* 1.3 63.0 + - - +
44C TYR 3.3 1.1 + - - -
45C ASN* 4.1 5.2 + - - +
46C ARG* 3.9 13.2 + - - +
93C LYS 4.1 17.8 + - - +
94C LEU* 3.9 33.6 - - + +
95C ARG 2.6 38.1 + - - +
96C TRP* 4.5 16.6 - - + -
139C LEU* 5.4 3.4 - - + -
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS 3.0 12.7 + - - -
42C ARG* 1.3 77.5 - - - +
44C TYR* 1.3 64.4 + - - +
45C ASN 3.4 0.2 - - - -
46C ARG* 3.2 25.3 + - - +
113C MET* 6.4 2.2 - - - -
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Residues in contact with TYR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.1 31.3 + - + +
41C PHE* 4.7 3.6 - - - +
42C ARG 3.3 2.0 - - - -
43C GLY* 1.3 78.9 - - - +
45C ASN* 1.3 60.5 + - + +
46C ARG 3.5 2.6 + - - +
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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