Contacts of the helix formed by residues 92 - 105 (chain C) in PDB entry 4QYJ
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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C LEU* 3.4 29.0 + - + +
89C LEU 3.4 4.9 + - - -
90C GLU 3.3 0.4 - - - -
91C VAL* 1.3 94.9 + - + +
93C GLY* 1.3 57.1 + - - +
94C ASP 3.7 1.3 - - - -
95C GLU* 3.5 12.7 + - + +
96C LEU* 3.3 30.7 + - + +
203C ARG* 4.0 20.6 + - - +
207C LEU* 3.5 23.3 - - + +
210C GLU* 4.0 16.6 + - - -
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Residues in contact with GLY 93 (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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89C LEU 3.3 14.1 + - - -
90C GLU 3.9 6.8 + - - -
91C VAL 3.3 4.6 + - - -
92C HIS* 1.3 74.8 - - - +
94C ASP* 1.3 64.1 + - - +
95C GLU 3.3 0.7 - - - -
96C LEU* 4.6 0.7 - - - -
97C ALA* 3.2 24.6 + - - +
112C LYS* 5.2 2.3 - - - +
116C VAL* 3.6 19.5 - - - +
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Residues in contact with ASP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C HIS 3.7 0.2 - - - -
93C GLY* 1.3 74.8 - - - +
95C GLU* 1.3 57.7 + - - +
97C ALA* 3.4 4.9 + - - +
98C ARG* 2.9 30.7 + - - +
108C LEU* 5.2 1.0 - - - +
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C HIS* 3.5 14.3 + - + +
93C GLY 3.3 0.6 - - - -
94C ASP* 1.3 74.9 - - - +
96C LEU* 1.3 61.2 + - + +
98C ARG* 3.3 5.6 + - - +
99C LEU* 2.9 31.7 + - - +
203C ARG* 5.8 6.3 - - - +
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Residues in contact with LEU 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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89C LEU* 3.5 44.4 - - + +
92C HIS* 3.3 19.3 + - + +
93C GLY* 4.6 0.2 - - - -
95C GLU* 1.3 76.3 - - + +
97C ALA* 1.3 61.3 + - - +
99C LEU* 3.3 12.0 + - + +
100C GLU* 3.1 24.6 + - - +
116C VAL* 3.9 16.6 - - + -
172C LEU* 4.4 12.8 - - + +
200C THR* 4.2 18.8 - - + +
203C ARG* 3.5 38.1 - - + +
204C LEU 5.0 0.7 - - - +
207C LEU* 4.1 10.5 - - + -
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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
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93C GLY 3.2 19.9 + - - +
94C ASP* 3.6 6.1 - - - +
96C LEU* 1.3 76.5 - - - +
98C ARG* 1.3 64.6 + - - +
100C GLU* 4.7 0.2 - - - -
101C THR* 3.2 24.6 + - - -
108C LEU* 3.8 11.8 - - + +
111C SER* 3.5 23.9 - - - +
112C LYS* 4.1 18.6 - - + +
116C VAL* 4.0 3.7 - - + +
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASP 2.9 19.6 + - - +
95C GLU* 3.3 5.4 + - - +
97C ALA* 1.3 71.7 - - - +
99C LEU* 1.3 58.5 + - - +
100C GLU 3.4 0.2 + - - -
101C THR* 3.5 3.9 + - - -
102C LEU* 2.9 40.9 + - + +
108C LEU* 4.1 13.8 - - + +
334C LEU* 5.0 10.3 - - + -
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 5.6 0.4 - - + -
95C GLU 2.9 16.3 + - - +
96C LEU* 3.4 15.5 - - + +
97C ALA 3.2 0.2 - - - -
98C ARG* 1.3 77.1 - - - +
100C GLU* 1.3 61.5 + - - +
102C LEU* 3.5 11.6 + - + +
103C ASN* 3.0 26.2 + - - +
199C LEU* 3.8 51.1 - - + +
200C THR* 4.2 14.6 - - + -
203C ARG* 4.3 19.3 - - + -
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU 3.1 12.4 + - - +
97C ALA* 4.0 1.3 - - - +
99C LEU* 1.3 76.1 - - - +
101C THR* 1.3 61.3 + - - +
103C ASN* 3.0 7.8 + - - +
104C ASN* 2.8 43.9 + - + +
106C LYS* 4.5 11.2 - - + +
111C SER* 3.6 17.9 - - - +
115C GLU* 4.6 11.2 - - + +
170C PHE 5.2 0.2 - - - -
171C PRO* 3.3 29.9 - - - +
172C LEU* 3.0 33.2 + - + +
200C THR* 3.4 19.4 + - + +
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Residues in contact with THR 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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36C ASN* 5.2 1.0 + - - +
37C PRO* 4.9 0.7 - - - +
97C ALA 3.2 12.0 + - - -
98C ARG 3.5 8.3 + - - -
100C GLU* 1.3 76.9 - - - +
102C LEU* 1.3 61.8 + - + +
105C GLY* 3.2 18.4 + - - -
106C LYS 3.2 28.2 + - - +
108C LEU* 3.3 19.1 - - - +
111C SER* 3.4 4.3 + - - -
333C GLY* 3.6 16.2 + - - +
334C LEU* 3.4 36.6 - - + -
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Residues in contact with LEU 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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36C ASN* 3.4 33.4 - - - +
37C PRO* 3.3 21.7 - - - +
43C LEU* 4.3 24.7 - - + -
98C ARG* 2.9 29.2 + - + +
99C LEU* 3.6 11.2 - - + +
101C THR* 1.3 73.8 - - + +
103C ASN* 1.3 56.3 + - - +
334C LEU* 4.1 23.1 - - + -
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Residues in contact with ASN 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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34C VAL* 2.9 33.2 - - - +
35C TYR 3.7 12.3 + - - +
37C PRO* 3.8 7.1 - - - +
43C LEU* 4.0 11.1 - - + +
99C LEU 3.0 15.6 + - - +
100C GLU* 3.0 10.1 + - - +
102C LEU* 1.3 73.1 - - - +
104C ASN* 1.3 59.9 + - + +
196C GLU 3.3 14.1 + - - +
197C THR* 3.3 31.3 - - - +
198C PRO* 3.7 3.5 - - - +
199C LEU* 3.9 16.6 + - + +
200C THR* 5.1 2.4 + - + -
344C VAL* 4.7 4.7 - - - +
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Residues in contact with ASN 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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37C PRO* 3.7 10.0 - - - +
100C GLU* 2.8 31.4 + - + +
103C ASN* 1.3 73.7 - - - +
105C GLY* 1.3 57.1 + - - +
106C LYS* 3.0 40.9 + - - +
168C TRP 2.8 29.7 + - - -
169C ASN 3.8 4.8 + - - +
171C PRO* 3.8 10.3 - - + +
197C THR* 4.3 3.2 - - + +
296C ASN* 5.4 0.2 - - - +
297C HIS* 5.3 2.3 - - - -
299C GLN* 5.4 2.4 + - - +
342C PRO 4.6 4.0 - - - +
343C MET 4.6 1.2 - - - +
344C VAL* 3.7 24.1 - - - +
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Residues in contact with GLY 105 (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 PRO* 3.8 14.9 - - - +
38C ALA* 5.8 2.0 - - - -
100C GLU 3.8 0.2 + - - -
101C THR 3.2 18.1 + - - -
104C ASN* 1.3 77.8 - - - +
106C LYS* 1.3 64.2 + - - +
297C HIS* 4.4 2.7 - - - -
333C GLY* 4.2 9.2 + - - -
341C GLY* 3.9 6.4 - - - -
342C PRO* 3.2 31.1 - - - +
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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