Contacts of the helix formed by residues 49 - 60 (chain C) in PDB entry 2Q2U
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 ASN 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C ILE* 3.1 5.8 + - + +
48C ARG* 1.3 73.3 - - - +
50C SER* 1.3 59.8 + - - +
51C VAL* 3.2 6.7 + - - +
52C MET* 2.6 38.1 + - - +
53C ASN* 3.1 17.5 + - - +
81C ALA 3.1 21.4 + - - +
82C VAL 3.3 12.9 + - - +
84C THR 3.2 15.3 + - - +
86C HIS* 3.7 17.4 - - - +
89C TYR* 3.4 28.9 - - - -
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Residues in contact with SER 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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47C ILE 4.6 0.4 + - - -
48C ARG 2.7 15.2 + - - -
49C ASN* 1.3 68.3 - - - +
51C VAL* 1.3 58.5 + - - +
53C ASN* 3.6 8.0 - - - +
54C ARG* 2.7 39.5 + - - +
85C GLY 5.8 0.9 - - - -
86C HIS 3.9 14.1 + - - -
87C LYS* 5.8 1.3 - - - -
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Residues in contact with VAL 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ASN* 3.2 6.7 + - - +
50C SER* 1.3 76.6 - - - +
52C MET* 1.3 58.5 + - - +
54C ARG* 4.0 14.1 + - - +
55C LEU* 2.9 52.8 + - + +
86C HIS 3.8 9.2 - - - +
87C LYS 3.6 19.7 - - - +
88C MET* 3.9 7.0 - - + -
89C TYR* 3.2 55.2 - - + +
93C PHE* 5.8 0.2 - - + -
131C GLN* 4.7 1.6 - - - +
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Residues in contact with MET 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 4.8 4.9 - - + -
49C ASN* 2.6 32.4 + - - +
51C VAL* 1.3 70.6 - - - +
53C ASN* 1.3 59.8 + - - +
55C LEU* 2.9 2.6 + - - +
56C LEU* 2.7 43.9 + - + +
68C ILE* 3.8 12.3 - - + -
70C ILE* 4.2 8.7 - - + -
81C ALA* 3.2 30.7 - - + +
82C VAL* 3.6 26.9 - - + -
89C TYR* 4.4 7.6 - - + -
93C PHE* 3.5 60.6 - - + -
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Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 3.3 20.7 + - - +
39C MET* 3.0 55.3 + - - +
46C PRO* 4.1 1.2 - - - +
47C ILE* 3.3 28.6 + - + +
49C ASN 3.1 9.6 + - - +
50C SER* 3.6 9.6 - - - +
52C MET* 1.3 78.0 - - - +
54C ARG* 1.3 59.7 - - - +
56C LEU* 3.5 0.4 + - - -
57C THR* 2.5 36.7 + - - -
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Residues in contact with ARG 54 (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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50C SER* 2.7 24.3 + - - +
51C VAL* 4.0 11.7 + - - +
53C ASN* 1.3 73.9 - - - +
55C LEU* 1.3 89.7 + - - +
57C THR* 3.1 15.6 + - - -
58C GLU* 2.8 57.0 + - + +
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Residues in contact with LEU 55 (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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51C VAL* 2.9 41.5 + - + +
52C MET* 2.9 5.1 + - - +
54C ARG* 1.3 93.2 - - - +
56C LEU* 1.3 62.6 + - - +
58C GLU* 3.0 26.1 + - - +
59C LEU* 2.9 25.3 - - + +
93C PHE* 4.3 4.5 - - + -
129C HIS* 3.7 26.7 - - + +
131C GLN* 3.7 21.3 - - - +
132C VAL* 3.8 23.6 - - + -
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Residues in contact with LEU 56 (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 MET* 3.6 35.0 - - + -
47C ILE* 6.1 0.2 - - + -
52C MET* 2.7 24.4 + - + +
55C LEU* 1.3 73.8 - - - +
57C THR* 1.3 55.2 + - - +
59C LEU* 4.5 3.6 - - + +
60C LEU* 2.8 58.5 + - + +
68C ILE* 4.0 20.0 - - + -
93C PHE* 4.3 14.6 - - + -
95C TYR* 3.8 31.2 - - + -
132C VAL* 3.8 19.1 - - + -
134C ILE* 5.1 4.5 - - + -
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Residues in contact with THR 57 (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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35C LYS* 3.3 29.6 + - - +
37C THR 3.3 23.6 - - - +
38C GLN* 3.7 10.7 - - - +
39C MET* 3.9 3.5 + - - +
53C ASN* 2.5 34.4 + - - -
54C ARG* 3.4 8.0 - - - -
55C LEU 3.1 0.4 - - - -
56C LEU* 1.3 76.7 - - - +
58C GLU* 1.3 60.1 + - + +
60C LEU 3.6 0.7 - - - +
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Residues in contact with GLU 58 (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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54C ARG* 2.8 47.2 + - - +
55C LEU* 3.0 21.7 + - - +
57C THR* 1.3 81.6 - - + +
59C LEU* 1.3 69.3 + - + +
60C LEU 4.8 0.5 - - - +
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Residues in contact with LEU 59 (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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55C LEU* 2.9 34.4 + - + +
56C LEU* 4.1 4.3 - - + +
58C GLU* 1.3 87.7 - - + +
60C LEU* 1.3 65.6 + - - +
61C PRO* 3.6 6.1 - - - +
119C TYR* 4.0 8.1 + - - -
125C HIS* 5.1 7.2 - - + +
126C ILE* 3.9 42.3 - - + +
129C HIS* 3.8 37.2 - - + +
132C VAL* 5.2 6.1 - - + -
134C ILE* 3.6 24.2 - - + -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LYS* 2.6 37.7 + - + +
39C MET* 3.8 15.3 - - + -
56C LEU* 2.8 43.0 + - + +
57C THR 3.6 2.9 - - - +
58C GLU 4.7 0.3 - - - -
59C LEU* 1.3 75.8 - - - +
61C PRO* 1.3 60.6 - - + +
64C SER* 3.5 23.6 - - - +
95C TYR* 3.4 46.4 - - + +
97C TRP* 4.1 16.8 - - + -
119C TYR* 4.9 0.2 - - - -
134C ILE* 4.5 14.8 - - + -
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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