Contacts of the helix formed by residues 45 - 52 (chain C) in PDB entry 7A62
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 HIS 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C PHE* 2.7 59.8 + + + +
42C ILE 3.1 6.4 + - - -
44C LYS* 1.3 101.9 + - + +
46C LEU* 1.3 59.3 + - - +
47C PRO* 3.4 4.5 - - - -
48C ASP* 3.4 22.2 + - + +
49C LEU* 2.8 42.4 + - + +
502C GOL 5.4 1.6 - - - -
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Residues in contact with LEU 46 (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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42C ILE* 3.3 23.1 - - + +
43C ALA* 3.7 12.8 - - - +
44C LYS 3.6 0.6 - - - -
45C HIS* 1.3 76.3 - - - +
47C PRO* 1.3 70.9 - - + +
49C LEU* 4.6 2.0 - - - +
50C ILE* 2.8 32.8 + - + +
55C LEU* 3.6 26.5 - - + -
85C CYS* 3.9 27.6 - - + +
86C ILE* 4.8 2.9 - - - -
89C ALA* 3.8 12.3 - - + -
152C PHE* 5.7 0.2 - - + -
153C SER 3.5 18.2 - - - +
154C PHE* 3.3 29.2 - - + +
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Residues in contact with PRO 47 (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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44C LYS 4.8 4.3 - - - +
45C HIS* 3.6 5.8 - - - -
46C LEU* 1.3 89.5 - - + +
48C ASP* 1.3 59.2 + - - +
50C ILE* 4.1 0.5 - - - +
51C GLU* 2.9 31.9 + - - +
153C SER* 3.9 16.8 - - - +
154C PHE 3.2 24.2 - - - +
155C ARG* 4.1 10.6 + - - +
156C ASP* 3.8 37.0 - - - +
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Residues in contact with ASP 48 (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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45C HIS* 3.4 25.6 + - + +
46C LEU 3.4 0.4 - - - -
47C PRO* 1.3 77.3 - - - +
49C LEU* 1.3 64.4 + - + +
51C GLU* 4.5 3.8 - - - +
52C SER* 2.7 35.5 + - - -
156C ASP* 4.9 7.1 - - - +
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Residues in contact with LEU 49 (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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41C PHE* 4.0 18.6 - - + -
42C ILE* 4.1 28.3 - - + +
45C HIS* 2.8 38.8 + - + +
46C LEU 4.2 0.9 - - - +
48C ASP* 1.3 77.5 - - + +
50C ILE* 1.3 61.4 + - - +
52C SER* 3.7 1.6 - - - -
53C GLY 3.1 1.0 + - - -
54C GLN* 2.8 57.1 + - + +
55C LEU* 3.1 21.5 + - + -
58C ARG* 4.3 24.0 - - + +
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Residues in contact with ILE 50 (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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46C LEU* 2.8 26.6 + - + +
49C LEU* 1.3 75.0 - - - +
51C GLU* 1.3 60.3 + - - +
53C GLY* 2.8 19.6 + - - -
55C LEU* 4.2 20.9 - - + -
89C ALA* 4.0 21.3 - - + -
93C GLY 3.6 24.5 - - - +
94C LYS* 3.2 21.7 + - + +
154C PHE* 4.0 7.0 - - - +
155C ARG* 3.5 45.3 - - - +
233C TYR* 3.8 8.3 - - + +
501C CL 4.2 2.4 - - - +
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Residues in contact with GLU 51 (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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47C PRO 2.9 20.7 + - - +
48C ASP* 4.0 4.3 - - - +
50C ILE* 1.3 75.8 - - - +
52C SER* 1.3 59.1 + - - +
94C LYS* 3.1 23.0 + - - +
155C ARG* 3.1 26.3 + - - +
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Residues in contact with SER 52 (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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48C ASP* 2.7 23.6 + - - -
49C LEU* 3.5 5.7 + - - -
51C GLU* 1.3 77.3 - - - +
53C GLY* 1.3 61.3 + - - +
54C GLN* 2.8 35.9 + - - +
94C LYS* 5.2 0.2 - - - -
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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