Contacts of the helix formed by residues 74 - 87 (chain C) in PDB entry 2XXA
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 PHE 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.7 21.5 - - + -
27C VAL* 4.3 19.7 - - + -
30C THR* 3.3 44.4 - - - -
31C LEU* 3.7 26.2 - - + -
34C VAL* 3.7 15.3 - - + -
55C VAL* 4.9 7.4 - - + +
59C ALA* 5.3 2.7 - - + -
70C PRO 4.1 5.6 - - - +
71C GLY* 3.3 30.3 - - - -
72C GLN 3.3 0.6 - - - -
73C GLU* 1.3 76.6 - - - +
75C VAL* 1.4 77.3 + - + +
76C LYS 3.2 2.0 - - - -
77C ILE* 3.2 24.5 + - + +
78C VAL* 3.2 26.6 + - + +
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Residues in contact with VAL 75 (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 VAL* 5.5 5.2 - - + -
71C GLY 3.5 24.2 - - - +
72C GLN* 3.5 14.1 - - - +
74C PHE* 1.4 85.0 - - + +
76C LYS* 1.4 54.1 + - - +
78C VAL* 3.1 11.4 + - + +
79C ARG* 2.8 32.9 + - + +
295C LEU* 5.6 6.5 - - + +
297C MET* 5.5 14.1 - - + -
300C VAL* 4.8 13.9 - - + -
301C LEU* 4.1 28.0 - - + -
304C ILE* 4.3 7.2 - - + -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASN* 3.1 29.8 + - - +
68C LEU* 4.6 4.9 - - - +
72C GLN 4.1 3.1 + - - +
73C GLU* 4.0 27.5 - - - +
74C PHE 3.2 0.4 - - - -
75C VAL* 1.4 78.2 - - - +
77C ILE* 1.4 52.7 + - + +
79C ARG* 3.4 7.3 + - - +
80C ASN* 2.8 53.0 + - - +
301C LEU* 5.5 4.3 - - + -
304C ILE* 3.9 21.3 - - + -
308C GLU* 3.5 36.7 + - - +
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Residues in contact with ILE 77 (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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22C LEU* 3.8 18.6 - - + -
55C VAL* 4.1 22.2 - - + +
58C LYS* 3.8 28.3 - - + -
59C ALA* 3.8 13.5 - - + +
63C GLU* 3.8 28.0 - - + +
73C GLU 3.6 20.4 - - - +
74C PHE* 3.2 16.7 + - - +
76C LYS* 1.4 73.3 - - + +
78C VAL* 1.4 62.9 + - - +
80C ASN* 4.7 4.0 - - - +
81C GLU* 3.3 30.1 + - + +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 5.8 0.9 - - + -
34C VAL* 3.8 31.4 - - + -
38C LEU* 5.7 1.8 - - + -
51C PHE* 4.1 17.4 - - + -
55C VAL* 4.0 26.0 - - + -
74C PHE* 3.4 30.7 - - + +
75C VAL* 3.1 12.0 + - + +
77C ILE* 1.4 77.4 - - - +
79C ARG* 1.4 56.9 + - - +
81C GLU 4.0 0.5 - - - -
82C LEU* 3.1 31.5 + - + +
295C LEU* 4.2 16.2 - - + -
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Residues in contact with ARG 79 (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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75C VAL* 2.8 19.7 + - + +
76C LYS* 3.7 5.8 - - - +
78C VAL* 1.4 70.2 - - - +
80C ASN* 1.3 74.4 + - - +
82C LEU* 3.3 12.9 + - - +
83C VAL* 3.3 27.9 + - + +
288C ASP* 4.9 10.3 + - - -
291C ALA* 5.9 1.8 - - + -
292C SER* 4.2 17.3 + - - +
295C LEU* 3.8 29.6 - - + +
301C LEU* 3.8 27.9 - - + +
305C GLU* 2.9 47.1 + - - +
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Residues in contact with ASN 80 (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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76C LYS* 2.8 40.6 + - - +
77C ILE* 4.6 4.5 - - - +
79C ARG* 1.3 81.5 + - - +
81C GLU* 1.3 62.9 + - + +
82C LEU 3.4 0.7 + - - -
83C VAL* 3.5 15.0 + - - +
84C ALA* 3.5 13.9 + - - +
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Residues in contact with GLU 81 (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 PHE* 3.8 18.6 - - + -
54C ARG* 3.6 34.2 + - + +
55C VAL* 5.1 6.1 - - + -
58C LYS* 3.6 38.3 + - + +
77C ILE* 3.3 29.3 + - + +
78C VAL* 5.1 0.2 - - - -
80C ASN* 1.3 76.3 - - + +
82C LEU* 1.3 58.2 + - - +
84C ALA* 4.2 7.3 - - - +
85C ALA* 3.2 28.9 + - - +
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Residues in contact with LEU 82 (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 LEU* 4.8 10.5 - - + -
51C PHE* 3.7 26.0 - - + -
78C VAL* 3.1 19.5 + - + +
79C ARG 3.4 7.0 - - - +
80C ASN 3.2 0.4 - - - -
81C GLU* 1.3 76.2 - - - +
83C VAL* 1.4 62.2 + - - +
85C ALA* 3.6 3.5 + - - +
86C MET* 3.2 27.2 + - + +
260C LEU* 3.8 30.6 - - + +
291C ALA* 3.4 40.2 - - + +
294C ILE* 4.7 12.1 - - + -
295C LEU* 4.1 16.8 - - + -
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Residues in contact with VAL 83 (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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79C ARG* 3.3 24.7 + - + +
80C ASN* 3.8 8.1 - - - +
81C GLU 3.5 0.4 - - - -
82C LEU* 1.4 75.7 - - - +
84C ALA* 1.3 58.5 + - - +
86C MET* 3.5 0.7 + - - -
87C GLY 3.1 28.0 + - - +
287C PRO* 3.7 24.1 - - + +
288C ASP* 4.4 24.7 - - + +
291C ALA* 3.8 22.7 - - + -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 5.2 3.1 - - - +
80C ASN 3.5 12.4 + - - +
81C GLU* 4.0 8.7 + - - +
82C LEU 3.5 0.4 - - - -
83C VAL* 1.3 76.0 - - - +
85C ALA* 1.4 61.7 + - - +
87C GLY 4.0 5.6 - - - -
88C GLU* 3.4 32.9 + - - +
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Residues in contact with ALA 85 (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 PHE* 4.3 7.6 - - + -
54C ARG* 3.5 33.1 - - - +
81C GLU 3.2 20.2 + - - +
82C LEU* 4.0 4.0 - - - +
84C ALA* 1.4 77.7 - - - +
86C MET* 1.4 58.8 + - - +
88C GLU* 5.3 2.2 - - - +
260C LEU* 4.8 8.5 - - + -
263C ARG* 3.2 25.5 + - - +
264C HIS* 5.5 0.7 + - - -
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Residues in contact with MET 86 (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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82C LEU* 3.2 19.2 + - - +
83C VAL 3.9 3.8 - - - +
85C ALA* 1.4 77.5 - - - +
87C GLY* 1.3 56.8 + - - +
259C ALA* 3.8 26.5 - - + +
260C LEU* 3.8 25.1 - - + -
263C ARG* 3.1 27.7 + - - +
270C ILE* 3.5 16.2 - - + +
285C PHE* 3.6 34.9 - - + -
287C PRO* 4.0 10.3 - - + +
290C ILE* 3.8 18.4 - - + -
291C ALA* 4.3 11.0 - - - -
294C ILE* 3.7 24.0 - - - -
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Residues in contact with GLY 87 (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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83C VAL* 3.1 19.0 + - - +
84C ALA* 3.6 7.7 - - - +
86C MET* 1.3 77.7 - - - +
88C GLU* 1.3 65.1 + - - +
89C GLU 3.3 10.3 + - - -
90C ASN 4.9 0.7 + - - -
263C ARG* 4.6 2.2 - - - -
269C PRO* 6.2 1.6 - - - -
285C PHE* 4.0 15.7 - - - -
287C PRO* 3.9 13.1 - - - +
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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