Contacts of the helix formed by residues 98 - 109 (chain C) in PDB entry 4X2Q
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 ASP 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C LEU 2.9 12.2 + - - +
95C VAL 3.3 3.8 - - - -
97C ARG* 1.3 119.9 + - - +
99C ARG* 1.3 61.7 + - - +
100C ALA* 3.3 2.7 - - - +
101C VAL* 3.6 20.1 - - + +
102C LEU* 3.2 28.1 + - + +
203C TYR* 2.7 30.5 + - + +
207C LEU* 3.4 10.4 - - + +
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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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95C VAL 3.1 9.0 + - - +
96C GLU* 3.3 40.6 + - - +
97C ARG 3.3 3.2 + - - -
98C ASP* 1.3 77.2 - - - +
100C ALA* 1.3 63.7 + - - +
103C ALA* 3.4 24.1 + - - +
118C PHE* 2.8 61.8 + - + -
119C TYR* 4.2 7.5 - - - +
122C LEU* 3.7 19.4 - - + +
123C GLN* 3.5 32.5 - - - +
126C ILE* 3.8 22.3 - - + +
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Residues in contact with ALA 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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10C SER 5.1 7.0 - - - +
12C THR* 4.0 18.8 - - + +
97C ARG 4.9 2.8 + - - +
98C ASP* 3.3 1.0 - - - +
99C ARG* 1.3 80.1 - - - +
101C VAL* 1.3 55.2 + - + +
104C THR* 2.5 32.9 + - - -
114C PHE* 3.6 8.1 - - - -
118C PHE* 3.7 16.0 - - + -
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Residues in contact with VAL 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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12C THR* 3.7 27.8 - - + +
15C LEU* 4.1 11.3 - - + +
98C ASP* 3.6 30.3 - - + +
100C ALA* 1.3 76.7 - - + +
102C LEU* 1.3 62.7 + - - +
104C THR* 3.3 8.5 + - - -
105C MET* 3.1 33.9 + - + +
203C TYR* 4.0 19.3 - - + +
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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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95C VAL* 3.8 37.9 - - + -
98C ASP 3.2 21.1 + - - +
101C VAL* 1.3 75.4 - - - +
103C ALA* 1.3 61.1 + - - +
105C MET* 3.5 8.0 + - + +
106C GLU* 3.1 27.2 + - - +
122C LEU* 3.7 15.5 - - + +
172C LEU* 3.9 21.7 - - + +
200C SER* 4.0 22.4 - - - +
203C TYR* 3.8 29.2 - - + -
204C MET* 4.6 4.5 - - + -
207C LEU* 4.1 14.6 - - + -
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Residues in contact with ALA 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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99C ARG 3.4 18.0 + - - +
102C LEU* 1.3 76.0 - - - +
104C THR* 1.3 56.9 + - - +
106C GLU* 3.4 2.2 + - - +
107C SER* 2.8 35.7 + - - -
114C PHE* 3.7 18.0 - - + -
117C ALA* 3.7 33.8 - - + +
118C PHE* 3.9 8.3 - - + +
122C LEU* 3.6 8.0 - - + +
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Residues in contact with THR 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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11C PRO* 4.2 2.0 - - + -
12C THR 3.5 27.9 + - - +
15C LEU* 3.8 28.5 - - + -
100C ALA 2.5 23.3 + - - -
101C VAL* 3.3 9.6 + - - -
102C LEU 3.3 0.6 - - - -
103C ALA* 1.3 74.6 - - - +
105C MET* 1.3 59.1 + - - +
107C SER* 3.4 2.4 + - - -
108C LEU* 2.8 31.4 + - - +
114C PHE* 3.3 15.2 - - - -
335C PHE* 3.8 23.4 - - + -
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Residues in contact with MET 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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15C LEU* 3.9 23.3 - - + +
16C GLU 5.3 6.1 - - - +
17C ILE* 4.3 18.2 - - + -
101C VAL* 3.1 26.1 + - + +
102C LEU* 3.7 9.9 - - + +
103C ALA 3.3 0.2 - - - -
104C THR* 1.3 76.8 - - - +
106C GLU* 1.3 54.7 + - - +
108C LEU* 4.3 1.8 - - - -
109C ASN* 2.6 40.2 + - - +
199C LEU* 3.7 37.2 - - + +
200C SER* 4.3 11.0 - - - +
203C TYR* 3.7 41.3 - - + -
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Residues in contact with GLU 106 (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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102C LEU 3.1 17.5 + - - +
103C ALA* 3.7 8.5 - - - +
105C MET* 1.3 76.3 - - - +
107C SER* 1.3 57.9 + - - +
109C ASN* 5.2 0.8 - - - +
110C GLY* 3.2 24.6 + - - +
111C GLY 3.6 1.7 + - - -
112C LYS* 4.0 9.5 + - + +
117C ALA* 4.4 10.5 - - + -
121C ASP* 3.8 24.1 - - + +
122C LEU* 5.1 3.4 - - + -
170C PHE 3.9 0.9 - - - -
171C PRO* 3.3 23.0 - - + +
172C LEU* 3.0 34.3 + - + +
173C LEU 4.4 0.5 + - - -
200C SER* 3.0 30.5 + - - -
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Residues in contact with SER 107 (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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103C ALA 2.8 18.4 + - - -
104C THR 3.8 3.8 - - - -
106C GLU* 1.3 77.0 - - - +
108C LEU* 1.3 62.6 + - - +
111C GLY* 3.3 18.9 + - - -
112C LYS 2.9 23.5 + - - -
113C PRO 4.5 0.4 - - - -
114C PHE* 3.4 20.4 + - - +
117C ALA* 4.8 0.9 - - - -
334C PRO* 3.3 36.8 + - - +
335C PHE* 4.3 6.9 + - - -
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Residues in contact with LEU 108 (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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15C LEU* 4.6 9.9 - - + -
17C ILE* 4.7 10.5 - - + -
41C ASN* 3.1 51.5 - - + +
42C PRO* 3.4 6.2 - - - +
46C GLU* 5.1 1.6 - - - +
48C VAL* 3.6 39.7 - - + -
104C THR 2.8 19.6 + - - +
105C MET* 3.7 4.0 - - - +
107C SER* 1.3 80.1 - - - +
109C ASN* 1.3 67.9 + - + +
199C LEU* 4.9 2.0 - - + -
335C PHE* 3.7 28.9 - - + -
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Residues in contact with ASN 109 (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 VAL* 3.4 12.9 - - - +
40C TYR 4.0 6.0 + - - +
41C ASN* 5.5 0.2 - - - +
42C PRO* 3.3 17.8 - - - +
48C VAL* 5.9 0.2 - - - -
105C MET 2.6 20.9 + - - +
106C GLU* 5.2 0.4 - - - -
108C LEU* 1.3 74.9 - - + +
110C GLY* 1.3 63.1 + - - +
196C GLN 2.9 22.9 + - - +
197C THR* 3.2 27.6 - - - +
198C PRO* 3.7 0.2 - - - +
199C LEU* 3.3 44.2 + - + +
200C SER* 4.7 2.4 + - - +
345C ILE* 4.2 3.5 - - - +
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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