Contacts of the helix formed by residues 94 - 104 (chain C) in PDB entry 4QY2
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 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B GLU* 4.3 21.8 + - - +
92C THR 3.6 0.8 + - - -
93C VAL* 1.3 90.5 - - + +
95C VAL* 1.3 65.0 + - - +
96C GLU 3.4 2.5 - - - -
97C ALA* 3.5 11.4 + - + +
98C LEU 3.2 15.4 + - - -
227C TRP* 3.6 19.8 + - + +
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Residues in contact with VAL 95 (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 HIS* 5.5 4.7 - - + -
57C ILE* 3.4 26.2 - - + -
86C TYR* 4.0 9.2 - - - +
92C THR* 3.3 31.1 + - - +
93C VAL 3.3 1.9 - - - -
94C ASN* 1.3 75.3 - - - +
96C GLU* 1.3 66.4 + - + +
98C LEU* 3.1 4.1 + - - +
99C ARG* 2.9 28.0 + - + +
394D SER* 6.6 0.2 - - - -
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Residues in contact with GLU 96 (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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399B GLN* 3.8 24.9 - - - +
94C ASN 3.4 0.4 - - - -
95C VAL* 1.3 85.4 - - + +
97C ALA* 1.3 63.3 + - - +
99C ARG* 2.5 50.7 + - - -
100C GLN* 2.9 54.3 + - - +
391D SER* 3.8 13.8 + - - -
394D SER* 4.0 9.5 + - - -
395D GLU 5.5 6.7 - - - +
396D ILE* 4.6 7.5 - - + +
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B GLU* 3.9 21.5 - - - +
398B HIS* 3.9 22.8 - - + -
399B GLN* 4.6 10.6 + - + +
94C ASN* 3.5 20.5 + - + +
95C VAL 3.3 0.2 - - - -
96C GLU* 1.3 79.3 - - - +
98C LEU* 1.3 60.0 + - - +
100C GLN* 3.6 3.1 + - - -
101C LYS* 3.2 23.9 + - - +
227C TRP* 4.3 12.6 - - + -
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Residues in contact with LEU 98 (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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57C ILE* 3.8 21.3 - - + -
60C LEU* 4.0 11.4 - - + -
92C THR* 4.1 7.4 - - + -
94C ASN 3.2 9.2 + - - +
95C VAL 3.1 10.1 + - - +
97C ALA* 1.3 77.4 - - - +
99C ARG* 1.3 66.2 + - - +
101C LYS* 3.1 7.4 + - + +
102C ILE* 3.0 34.1 + - + +
170C LEU* 3.8 24.5 - - + -
172C MET* 3.8 22.9 - - + -
227C TRP* 3.6 44.8 - - + +
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Residues in contact with ARG 99 (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 HIS* 3.9 24.9 - - + -
56C PRO* 4.4 7.4 - - + -
57C ILE* 4.1 12.7 - - + +
79C GLU* 3.0 36.3 + - - +
95C VAL* 2.9 16.3 + - + +
96C GLU* 2.5 45.9 + - - +
98C LEU* 1.3 74.4 - - - +
100C GLN* 1.3 65.3 + - - +
102C ILE* 3.3 6.0 + - - +
103C MET* 2.9 53.6 + - - +
261C GLN* 3.6 18.1 + - - +
388D SER* 5.0 7.9 + - - -
390D GLU 5.0 1.6 - - - +
391D SER* 3.7 19.4 + - - +
394D SER* 4.5 5.2 - - - -
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Residues in contact with GLN 100 (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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398B HIS* 4.2 2.6 - - + -
399B GLN* 4.1 24.0 - - - +
402B ASN* 2.7 44.8 + - - +
96C GLU* 2.9 53.1 + - - +
97C ALA* 3.9 4.3 - - - +
99C ARG* 1.3 83.8 - - - +
101C LYS* 1.3 61.5 + - - +
103C MET* 3.3 7.5 + - - +
104C GLU* 3.1 31.1 + - - +
388D SER 4.5 9.1 + - - +
389D ILE* 4.4 20.2 + - - +
396D ILE* 5.8 0.4 - - - +
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Residues in contact with LYS 101 (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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398B HIS* 3.1 47.8 + - + +
97C ALA 3.2 14.3 + - - +
98C LEU* 3.1 7.3 + - + +
100C GLN* 1.3 79.8 - - - +
102C ILE* 1.3 60.0 + - + +
104C GLU* 3.5 12.5 + - + +
105C SER* 3.6 8.3 + - - -
168C GLU* 6.0 0.7 - - - +
170C LEU* 4.2 22.4 - - + -
227C TRP* 3.6 30.8 - - + -
229C LEU* 4.2 21.5 - - + +
253C LEU* 3.6 18.0 - - + +
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Residues in contact with ILE 102 (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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56C PRO* 3.6 42.2 - - + +
57C ILE* 4.0 13.5 - - + -
59C MET* 4.2 17.0 - - - -
60C LEU* 3.6 33.0 - - + -
74C TRP* 5.3 0.2 - - + -
77C LEU* 3.9 11.0 - - + +
98C LEU* 3.0 22.6 + - + +
99C ARG* 3.7 5.4 - - - +
101C LYS* 1.3 77.9 - - - +
103C MET* 1.3 56.3 + - - +
104C GLU 3.1 0.4 - - - -
105C SER* 2.7 28.9 + - - +
108C ILE* 4.5 11.7 - - + -
253C LEU* 4.1 15.5 - - + -
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Residues in contact with MET 103 (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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56C PRO* 4.0 12.8 - - + -
77C LEU* 3.7 32.0 - - - +
79C GLU* 3.7 27.6 - - + +
99C ARG* 2.9 39.3 + - - +
100C GLN* 3.3 8.2 + - - +
102C ILE* 1.3 76.8 - - - +
104C GLU* 1.3 59.2 + - - +
105C SER 3.5 1.7 - - - +
257C GLY 3.7 2.3 - - - +
258C LEU 3.8 0.9 - - - -
259C GLY* 3.1 31.2 + - - +
260C ILE 3.6 41.5 - - - +
261C GLN* 4.3 3.4 - - + -
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Residues in contact with GLU 104 (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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398B HIS* 3.2 18.3 + - + -
402B ASN* 3.1 29.3 + - - +
100C GLN* 3.1 18.2 + - - +
101C LYS* 3.7 9.6 - - + +
102C ILE 3.1 0.4 - - - -
103C MET* 1.3 77.0 - - - +
105C SER* 1.3 59.8 + - - +
255C GLY 3.9 0.5 - - - +
256C ARG* 3.3 19.1 - - + +
257C GLY 3.0 24.2 + - - +
387D GLU* 3.4 34.6 - - + +
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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