Contacts of the helix formed by residues 104 - 119 (chain C) in PDB entry 7A62
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 PRO 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C VAL* 4.3 18.8 - - + +
60C GLU* 4.3 14.6 - - + -
90C TYR* 3.5 34.8 - - + +
102C VAL* 3.5 9.4 - - + +
103C LEU* 1.3 93.3 - - + +
105C ARG* 1.3 67.2 + - - +
106C ASN* 4.4 5.2 - - + +
107C ILE* 3.0 7.8 + - + +
108C ALA 2.9 20.1 + - - -
250C GLU* 3.6 9.0 - - - +
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Residues in contact with ARG 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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64C MET* 3.6 26.5 - - + +
103C LEU 3.5 0.6 + - - -
104C PRO* 1.3 71.8 - - - +
106C ASN* 1.3 68.8 + - - +
107C ILE 3.1 1.4 + - - -
109C VAL* 3.1 32.4 + - + +
110C PRO* 3.9 0.2 - - - +
250C GLU* 2.8 45.2 + - + +
251C GLY* 3.8 25.0 + - - -
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Residues in contact with ASN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TRP* 4.8 4.5 + - - -
59C VAL 5.4 2.7 - - - +
60C GLU 5.6 0.8 + - - -
62C LEU* 2.7 35.1 + - + +
63C ASN* 3.6 21.7 - - - +
64C MET* 3.3 39.0 - - - +
65C LEU 4.8 0.2 + - - -
104C PRO* 3.2 4.1 - - + +
105C ARG* 1.3 84.1 + - - +
107C ILE* 1.3 63.4 + - - +
110C PRO* 3.5 16.3 - - - +
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Residues in contact with ILE 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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39C TRP* 4.5 4.9 - - - +
59C VAL* 3.9 26.9 - - + +
62C LEU* 3.7 24.0 - - + -
83C LEU* 3.8 26.5 - - + +
86C ILE* 4.2 18.4 - - + -
87C THR* 3.9 21.3 - - - +
103C LEU* 3.9 16.6 - - + -
104C PRO* 3.0 8.2 + - + +
106C ASN* 1.3 82.6 - - - +
108C ALA* 1.3 60.5 + - - +
109C VAL 3.3 1.8 - - - -
110C PRO* 3.3 5.9 - - - +
111C TYR* 2.9 35.8 + - + +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 3.6 32.5 - - + +
104C PRO 2.9 16.0 + - - +
107C ILE* 1.3 77.4 - - - +
109C VAL* 1.3 57.7 + - - +
111C TYR* 3.8 2.2 - - - -
112C CYS* 2.8 36.5 + - - +
249C TYR* 3.8 15.5 - - + -
250C GLU 3.7 19.1 - - - +
252C PHE* 5.1 0.4 - - - -
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Residues in contact with VAL 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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64C MET* 4.2 13.7 - - + -
105C ARG* 3.1 22.5 + - + +
108C ALA* 1.3 76.0 - - - +
110C PRO* 1.3 72.1 - - + +
112C CYS* 3.2 2.4 + - - +
113C GLN* 2.9 50.2 + - + +
250C GLU 3.6 14.8 - - - +
251C GLY* 3.5 29.2 - - - +
252C PHE* 4.1 11.2 - - + +
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Residues in contact with PRO 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TRP* 4.1 14.4 - - + -
64C MET* 3.6 17.3 - - - -
65C LEU 3.7 18.8 - - - +
66C SER* 5.6 0.2 - - - -
67C ILE* 3.7 22.9 - - + +
83C LEU* 4.3 2.6 - - + +
105C ARG 3.9 0.2 - - - +
106C ASN 3.5 15.0 - - - +
107C ILE* 3.3 14.8 - - - +
109C VAL* 1.3 94.9 - - + +
111C TYR* 1.3 59.4 + - - +
113C GLN* 3.9 12.1 - - - +
114C LEU* 3.0 26.7 + - - +
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Residues in contact with TYR 111 (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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80C ARG* 4.1 20.0 + - + -
83C LEU* 3.6 29.5 - - + +
84C GLY* 3.4 25.0 - - - -
87C THR* 3.5 32.3 - - + -
103C LEU* 4.3 10.1 - - + -
107C ILE* 2.9 21.7 + - + +
108C ALA 3.8 2.7 - - - +
110C PRO* 1.3 76.8 - - - +
112C CYS* 1.3 58.4 + - - +
114C LEU* 3.7 1.9 + - + +
115C SER* 2.8 46.3 + - - -
122C PRO* 3.6 27.8 - - + -
123C ILE* 3.1 31.8 + - - -
124C LEU* 4.3 0.2 - - - -
249C TYR* 4.8 2.5 - + - -
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Residues in contact with CYS 112 (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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108C ALA 2.8 24.5 + - - +
111C TYR* 1.3 76.4 - - - +
113C GLN* 1.3 64.8 + - - +
115C SER* 4.0 5.0 - - - -
116C ALA* 3.1 23.6 + - - +
122C PRO* 4.0 9.0 - - - -
249C TYR* 3.4 35.9 - - - -
252C PHE* 3.5 42.2 - - + -
253C TRP* 4.0 11.6 - - + -
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Residues in contact with GLN 113 (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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66C SER* 6.0 0.3 - - - -
67C ILE* 3.6 29.2 + - + +
109C VAL* 2.9 38.1 + - - +
110C PRO* 3.9 8.0 - - - +
112C CYS* 1.3 74.0 - - - +
114C LEU* 1.3 66.6 + - - +
116C ALA* 3.3 6.5 + - - +
117C ALA* 3.1 22.3 + - - +
252C PHE* 4.0 17.3 - - + -
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Residues in contact with LEU 114 (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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67C ILE* 4.5 14.6 - - + +
70C LEU* 4.2 11.4 - - + -
76C GLN* 3.8 43.3 - - + +
79C ALA* 3.6 18.4 - - + +
80C ARG* 3.6 34.1 - - + +
83C LEU* 4.1 11.4 - - + -
110C PRO 3.0 17.5 + - - +
111C TYR* 4.0 3.6 - - + +
113C GLN* 1.3 77.8 - - - +
115C SER* 1.3 57.8 + - - +
117C ALA* 3.1 8.3 + - + +
118C LEU* 2.9 33.6 + - + +
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Residues in contact with SER 115 (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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80C ARG* 2.9 26.8 + - - +
111C TYR* 2.8 33.8 + - - -
112C CYS* 4.0 3.6 - - - -
113C GLN 3.3 0.2 - - - -
114C LEU* 1.3 77.1 - - - +
116C ALA* 1.3 52.4 + - - +
118C LEU* 3.2 4.2 + - - +
119C GLU 2.6 30.0 + - - -
120C LEU 2.9 30.0 + - - +
122C PRO* 3.7 14.1 - - - +
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Residues in contact with ALA 116 (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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112C CYS 3.1 18.7 + - - +
113C GLN* 3.6 6.3 - - - +
115C SER* 1.3 75.7 - - - +
117C ALA* 1.3 61.9 + - - +
119C GLU* 3.2 17.9 + - - +
120C LEU 5.0 0.4 - - - -
252C PHE* 5.4 6.7 - - + -
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Residues in contact with ALA 117 (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 GLN* 4.8 15.3 - - - +
113C GLN 3.1 12.9 + - - +
114C LEU* 3.1 11.0 + - + +
116C ALA* 1.3 78.2 - - - +
118C LEU* 1.3 63.7 + - + +
119C GLU* 3.7 8.5 + - - +
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Residues in contact with LEU 118 (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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73C HIS* 4.1 29.2 - - + +
76C GLN* 3.9 44.2 - - + +
77C ARG* 4.3 9.6 - - - +
80C ARG* 3.6 37.2 - - + -
114C LEU* 2.9 19.8 + - + +
115C SER 4.0 2.7 - - - +
117C ALA* 1.3 79.7 - - + +
119C GLU* 1.3 73.3 + - - +
120C LEU* 3.2 9.0 + - + +
301C PRO* 3.3 19.4 - - - +
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Residues in contact with GLU 119 (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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115C SER 2.6 12.8 + - - -
116C ALA* 3.2 15.7 + - - +
117C ALA 4.1 6.8 - - - +
118C LEU* 1.3 79.5 - - - +
120C LEU* 1.3 56.5 + - - +
297C ARG 4.7 0.3 - - - +
301C PRO* 3.7 25.3 - - + +
304C ARG* 3.0 36.3 + - - +
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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