Contacts of the helix formed by residues 37 - 48 (chain C) in PDB entry 4CYM
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 GLY 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C GLY 3.4 0.6 - - - -
36C VAL* 1.3 80.0 - - - +
38C LYS* 1.3 58.1 + - - +
40C SER* 2.9 2.1 + - - -
41C ILE* 2.8 41.4 + - - +
143C ASN* 3.7 3.4 - - - -
1198C GCP 3.0 40.7 + - - -
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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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30C VAL* 3.7 24.4 - - + +
31C ILE* 3.3 34.3 - - - -
32C GLY* 2.9 11.6 + - - +
33C GLU 2.8 18.6 + - - -
36C VAL* 3.8 13.8 - - + +
37C GLY* 1.3 77.7 - - - +
39C THR* 1.3 64.6 + - - +
41C ILE* 3.4 7.6 + - - +
42C ILE* 3.3 25.4 + - - +
81C ASP* 3.8 9.9 - - - +
82C ILE 2.9 26.9 - - - -
84C GLY 3.8 0.4 - - - +
105C VAL* 4.2 5.4 - - + -
1198C GCP 2.3 49.0 + - - +
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Residues in contact with THR 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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38C LYS* 1.3 77.4 - - - +
40C SER* 1.3 57.6 + - - +
42C ILE* 3.3 6.0 + - - +
43C LYS* 2.9 31.2 + - + +
55C ARG 5.7 3.4 - - - +
57C THR* 2.8 6.0 + - - +
61C ASP* 5.0 8.3 - - - +
81C ASP* 2.5 25.3 + - - +
1198C GCP 2.9 15.8 + - - +
1199C MG 2.2 30.1 - - - -
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Residues in contact with SER 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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37C GLY 2.9 7.4 + - - -
39C THR* 1.3 72.6 - - - +
41C ILE* 1.3 67.6 + - - +
43C LYS* 3.2 8.4 + - - +
44C ARG* 2.9 25.5 + - - +
49C LEU 4.3 1.7 - - - +
50C PHE* 4.3 9.5 - - - +
51C SER 4.6 3.4 + - - -
175C ALA* 3.7 11.9 - - - +
1198C GCP 2.9 52.6 + - - -
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Residues in contact with ILE 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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30C VAL* 5.6 3.8 - - + -
37C GLY 2.8 23.7 + - - +
38C LYS* 3.6 5.8 - - - +
40C SER* 1.3 75.5 - - - +
42C ILE* 1.3 71.0 + - + +
44C ARG* 3.1 2.3 + - - +
45C TYR* 2.8 23.7 + - + +
103C PHE* 6.1 4.5 - - + -
105C VAL* 3.9 31.4 - - + -
141C LEU* 3.9 24.5 - - + -
143C ASN* 3.9 26.9 - - + +
173C THR* 4.5 1.8 - - - +
175C ALA* 3.8 8.9 - - + +
181C ILE* 4.3 28.2 - - + +
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Residues in contact with ILE 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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30C VAL* 3.7 30.3 - - + -
38C LYS 3.3 13.8 + - - +
39C THR* 3.3 8.5 + - - +
41C ILE* 1.3 82.9 - - + +
43C LYS* 1.3 63.9 + - - +
45C TYR* 3.3 5.3 + - - -
46C VAL* 3.0 25.2 + - + +
62C PHE 5.6 0.2 - - - -
63C ALA* 3.7 31.0 - - + +
79C LEU* 4.0 25.6 - - + +
81C ASP* 3.4 36.8 - - + +
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Residues in contact with LYS 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 THR* 2.9 21.7 + - + +
40C SER* 3.7 7.6 - - - +
41C ILE 3.1 0.2 - - - -
42C ILE* 1.3 77.8 - - - +
44C ARG* 1.3 58.3 + - - +
47C HIS* 2.8 42.6 + - + +
48C GLN 3.5 1.0 + - - -
49C LEU* 3.7 38.3 + - + +
50C PHE* 4.5 3.5 - - - +
51C SER* 4.1 25.4 - - - +
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Residues in contact with ARG 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 SER 2.9 12.4 + - - +
41C ILE 3.5 7.0 - - - +
43C LYS* 1.3 75.2 - - - +
45C TYR* 1.3 64.8 + - - +
48C GLN* 2.7 75.8 + - - +
49C LEU* 3.2 22.7 + - - +
50C PHE* 3.8 14.6 - - - +
175C ALA 2.5 27.0 + - - +
176C LYS 3.4 17.9 + - - -
178C ASN* 3.5 39.5 - - - +
181C ILE* 3.9 15.7 - - + -
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Residues in contact with TYR 45 (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 ILE* 2.8 20.7 + - + +
42C ILE* 3.8 5.4 - - - +
44C ARG* 1.3 76.8 - - - +
46C VAL* 1.3 57.0 + - + +
48C GLN* 4.0 8.6 + - - +
65C LYS* 3.0 54.8 + - + +
67C LEU* 3.8 20.3 - - - +
77C LEU* 4.4 12.3 - - + +
79C LEU* 4.2 19.1 - - + -
103C PHE* 6.3 3.1 - + - -
181C ILE* 3.6 24.9 - - + -
182C GLU* 3.6 33.6 + - + -
185C ALA* 3.3 32.0 - - + +
186C ARG 5.1 0.2 + - - -
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Residues in contact with VAL 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* 3.0 22.7 + - + +
44C ARG 3.0 0.4 - - - -
45C TYR* 1.3 83.9 - - + +
47C HIS* 1.3 90.9 + - + +
48C GLN* 3.7 2.2 - - - -
63C ALA* 4.5 8.1 - - + -
64C LEU 3.8 19.1 - - - +
65C LYS* 4.2 23.4 + - + -
79C LEU* 4.1 23.6 - - + -
586F GLN* 6.1 0.7 - - - +
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Residues in contact with HIS 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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43C LYS* 2.8 25.2 + - + +
46C VAL* 1.3 103.2 - - + +
48C GLN* 1.3 73.6 + - - +
49C LEU* 3.1 27.3 + - + +
63C ALA* 5.2 8.3 - - + -
586F GLN* 4.4 23.2 + - - -
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Residues in contact with GLN 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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44C ARG* 2.7 48.5 + - - +
45C TYR* 4.0 14.1 + - - +
46C VAL 5.4 1.3 - - - +
47C HIS* 1.3 81.0 - - - +
49C LEU* 1.3 63.7 + - - +
65C LYS* 5.4 1.4 - - - +
178C ASN* 2.9 30.7 + - - +
182C GLU* 4.2 15.8 + - - +
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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