Contacts of the helix formed by residues 96 - 113 (chain C) in PDB entry 1HGC
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 VAL 96 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ASP* 4.6 0.9 - - - +
101B GLU* 3.6 31.9 - - + +
94C ASP* 2.9 21.3 + - - +
95C PRO* 1.3 77.2 - - - +
97C ASN* 1.3 77.1 + - - +
98C PHE 3.3 0.2 - - - -
99C LYS* 3.4 31.0 - - + +
100C LEU* 3.7 16.1 - - + +
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Residues in contact with ASN 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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99B ASP* 2.8 30.3 + - - +
32C MET* 4.7 1.2 - - - +
38C THR* 4.8 2.8 + - - -
39C THR* 3.6 27.0 - - + +
42C TYR* 3.4 18.0 + - - -
93C VAL* 3.7 13.9 - - + -
94C ASP* 2.8 23.3 + - - +
96C VAL* 1.3 78.7 - - - +
98C PHE* 1.3 65.7 - - - +
99C LYS 3.0 2.9 - - - -
100C LEU* 3.1 24.1 + - - +
101C LEU* 3.2 10.0 + - - +
142C HEM 3.4 17.5 - - + +
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 3.8 26.5 - + + -
93C VAL* 4.2 14.4 - - + -
94C ASP 4.3 1.3 - - - -
95C PRO* 3.2 16.9 + - + +
97C ASN* 1.3 78.4 - - - +
99C LYS* 1.3 58.4 + - + +
101C LEU* 3.7 2.0 + - - +
102C SER* 2.8 33.2 + - - -
133C SER* 3.5 30.8 + - - +
136C LEU* 3.5 23.3 - - + -
137C THR* 3.3 32.8 - - + -
140C TYR* 3.7 14.1 - - - -
142C HEM 3.3 44.6 - + + +
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO 4.3 5.6 - - - +
96C VAL* 3.4 28.9 - - + +
98C PHE* 1.3 80.4 - - + +
100C LEU* 1.3 70.0 + - + +
102C SER* 3.6 5.8 + - - -
103C HIS* 3.3 22.5 + - - +
130C ALA* 6.1 3.2 - - - +
133C SER* 6.4 0.7 - - - -
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Residues in contact with LEU 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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32C MET* 4.3 1.8 - - - -
36C PHE* 4.0 42.6 - - + -
38C THR* 4.9 6.3 - - - +
39C THR* 3.9 25.8 - - + -
96C VAL* 3.7 21.5 - - + +
97C ASN* 3.5 17.5 - - - +
99C LYS* 1.3 80.0 - - + +
101C LEU* 1.3 63.5 - - - +
103C HIS* 3.7 5.9 + - + +
104C CYS* 3.1 32.0 + - - -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 4.5 24.7 - - + +
29C LEU* 4.5 17.0 - - + -
32C MET* 3.6 23.3 - - + -
62C VAL* 4.8 8.3 - - + -
97C ASN 3.2 10.7 + - - +
98C PHE* 4.1 3.1 - - - +
100C LEU* 1.3 76.5 - - - +
102C SER* 1.3 68.5 + - - +
104C CYS* 3.2 1.5 + - - -
105C LEU* 3.0 33.6 + - + +
142C HEM 3.7 48.0 - - + -
150C OXY 4.0 13.5 - - - +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE 2.8 22.6 + - - -
99C LYS* 3.8 8.1 - - - -
101C LEU* 1.3 78.1 - - - +
103C HIS* 1.3 61.2 + - - +
105C LEU* 3.2 12.0 + - - +
106C LEU* 3.0 23.5 + - - +
126C ASP* 5.9 3.1 - - - -
129C LEU* 3.6 34.6 + - - +
130C ALA* 5.4 0.6 - - - -
133C SER* 3.5 15.1 + - - -
142C HEM 5.1 3.7 - - - +
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Residues in contact with HIS 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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36C PHE* 4.0 13.5 - - + -
99C LYS 3.3 15.7 + - - +
100C LEU* 3.7 7.0 - - + +
101C LEU 3.2 0.4 - - - -
102C SER* 1.3 80.1 - - - +
104C CYS* 1.3 56.4 + - - +
106C LEU* 3.0 15.4 - - + +
107C VAL* 2.9 34.8 + - + +
108D ASN* 3.5 51.3 + - + +
111D VAL* 4.0 7.8 - - + +
112D CYS* 4.2 7.6 - - - -
127D GLN* 3.9 9.9 + - - -
131D GLN* 2.7 31.2 + - - -
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Residues in contact with CYS 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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28C ALA* 3.4 21.1 - - - +
31C ARG* 3.9 9.3 - - + -
32C MET* 3.4 33.4 - - + +
36C PHE* 3.6 17.0 - - - -
100C LEU 3.1 22.8 + - - +
101C LEU* 3.2 6.0 + - - +
103C HIS* 1.3 77.6 - - - +
105C LEU* 1.3 59.7 + - - +
107C VAL* 4.4 5.4 - - - +
108C THR* 2.8 33.6 + - - -
127D GLN* 4.0 11.2 - - - +
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Residues in contact with LEU 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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14C TRP* 5.6 7.4 - - + -
24C TYR* 4.4 9.4 - - + +
25C GLY* 4.7 8.1 - - - -
28C ALA* 3.2 24.5 - - + -
62C VAL* 5.0 4.9 - - + -
66C LEU* 3.5 33.0 - - + -
101C LEU* 3.0 28.8 + - + +
102C SER* 3.2 7.8 + - - +
104C CYS* 1.3 76.2 - - - +
106C LEU* 1.3 57.3 + - - +
108C THR* 3.8 4.9 - - + -
109C LEU* 2.9 44.2 + - + +
129C LEU* 4.2 20.2 - - + -
142C HEM 4.9 5.4 - - + -
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Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C SER* 3.0 11.0 + - - +
103C HIS* 3.0 22.2 - - + +
105C LEU* 1.3 75.5 - - - +
107C VAL* 1.3 57.2 + - - -
109C LEU* 3.5 4.7 + - + +
110C ALA* 2.9 30.6 + - - +
117C PHE* 4.1 22.0 - - + -
122C HIS* 4.2 15.0 - - + +
125C LEU* 4.2 22.0 - - + -
126C ASP* 3.3 33.4 - - + +
129C LEU* 3.6 26.7 - - + -
35D TYR* 5.4 1.8 - - - +
112D CYS* 4.2 12.8 - - - -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 3.8 14.8 - - - +
103C HIS* 2.9 43.0 + - + +
104C CYS 4.1 4.0 - - - +
106C LEU* 1.3 75.0 - - - +
108C THR* 1.3 65.3 + - - +
110C ALA* 2.9 9.3 + - - +
111C ALA* 2.9 24.4 + - - +
111D VAL* 4.0 10.8 - - + -
112D CYS* 4.0 14.1 - - - -
115D ALA* 3.7 20.1 - - + +
122D PHE* 4.0 8.3 - - + -
127D GLN* 3.7 24.7 - - - +
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Residues in contact with THR 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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24C TYR* 3.5 45.8 - - + +
27C GLU* 3.8 18.4 - - - +
28C ALA* 3.4 13.0 + - + -
31C ARG* 3.3 19.8 + - - +
104C CYS 2.8 22.1 + - - -
105C LEU* 3.8 9.9 - - + +
107C VAL* 1.3 77.8 - - - +
109C LEU* 1.3 63.9 + - + +
111C ALA* 3.3 1.5 + - - +
112C HIS* 2.9 29.8 + - + -
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Residues in contact with LEU 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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13C ALA* 6.1 0.7 - - + -
14C TRP* 4.4 18.4 - - + -
17C VAL* 3.9 28.7 - - + -
24C TYR* 4.3 13.9 - - + -
105C LEU* 2.9 30.4 + - + +
106C LEU* 3.6 9.4 - - + +
108C THR* 1.3 79.0 - - + +
110C ALA* 1.3 62.6 + - - +
112C HIS* 4.9 1.6 - - - -
113C LEU* 2.8 47.5 + - + +
117C PHE* 4.7 8.5 - - + +
125C LEU* 3.9 33.2 - - + -
129C LEU* 5.3 4.7 - - + -
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Residues in contact with ALA 110 (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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106C LEU 2.9 18.4 + - - +
107C VAL* 2.9 8.5 + - - +
109C LEU* 1.3 78.6 - - - +
111C ALA* 1.3 61.0 + - - +
112C HIS 3.5 0.3 + - - -
114C PRO* 3.6 10.7 - - - +
117C PHE* 3.5 36.8 - - + -
112D CYS* 3.9 17.0 - - + +
115D ALA* 4.4 0.4 - - + -
116D HIS* 3.5 28.4 - - - +
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Residues in contact with ALA 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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31C ARG* 4.7 12.8 - - - +
107C VAL 2.9 14.8 + - - +
108C THR 3.6 5.2 - - - +
110C ALA* 1.3 78.1 - - - +
112C HIS* 1.3 69.1 + - + +
114C PRO* 4.4 4.8 - - - +
115D ALA* 3.7 26.2 + - + +
119D GLY* 3.4 32.5 - - - +
120D LYS* 4.0 3.6 + - - -
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Residues in contact with HIS 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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24C TYR* 3.5 45.7 + + + +
27C GLU* 2.6 40.4 + - - -
108C THR* 2.9 27.8 + - + +
109C LEU* 4.2 2.5 - - - +
111C ALA* 1.3 84.3 + - + +
113C LEU* 1.3 66.9 + - + +
114C PRO* 3.1 11.0 - - - +
120D LYS* 4.1 31.5 + - - -
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Residues in contact with LEU 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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13C ALA* 3.7 32.3 - - + +
16C LYS* 4.2 26.9 - - + +
17C VAL* 4.2 13.7 - - + -
24C TYR* 4.6 10.3 - - + +
109C LEU* 2.8 28.9 + - + +
110C ALA 4.0 3.4 - - - -
112C HIS* 1.3 85.7 - - + +
114C PRO* 1.3 66.9 - - - +
115C ALA 3.4 2.2 - - - -
116C GLU* 3.1 33.0 + - + +
117C PHE* 3.0 23.2 + - + +
125C LEU* 6.2 0.9 - - + -
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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
------------------------------------------------------------
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