Contacts of the helix formed by residues 89 - 108 (chain C) in PDB entry 2H4C
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 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASP* 6.1 0.2 - - - -
86C ASP* 2.9 19.5 + - - +
88C ASN* 1.3 76.4 + - - +
90C LEU* 1.3 68.3 + - - +
91C CYS* 3.4 14.4 + - - +
92C LEU* 3.4 38.6 + - + +
93C LYS* 3.0 17.5 + - - +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASN* 5.0 11.0 - - + +
58C ASP* 5.5 7.6 - - + +
89C ASN* 1.3 74.8 + - - +
91C CYS* 1.3 64.4 + - - +
93C LYS* 3.2 36.9 - - - +
94C THR* 3.4 16.1 - - + +
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Residues in contact with CYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 3.2 17.4 - - - +
56C ASN 2.9 21.8 - - - +
58C ASP* 3.6 13.7 - - + -
59C CYS* 2.0 64.6 - - + -
89C ASN* 3.4 7.2 + - - +
90C LEU* 1.3 77.9 - - - +
92C LEU* 1.3 61.6 + - + +
94C THR* 3.1 18.8 + - - -
95C VAL* 3.6 4.3 - - - +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C CYS* 5.0 4.0 - - + -
71C ALA* 4.0 12.3 - - + -
72C THR 3.9 29.8 - - - +
73C TYR* 4.1 11.9 - - + +
86C ASP* 2.8 32.5 - - - +
89C ASN* 3.4 34.7 + - + +
90C LEU 3.3 0.6 - - - -
91C CYS* 1.3 77.9 - - + +
93C LYS* 1.3 63.9 + - - +
95C VAL* 2.8 20.6 + - - +
96C CYS* 3.1 8.8 + - - +
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Residues in contact with LYS 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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84C CYS* 5.2 5.6 - - + -
86C ASP* 2.7 34.9 + - + +
89C ASN 3.0 13.9 + - - +
90C LEU* 3.2 35.7 - - - +
92C LEU* 1.3 73.0 - - - +
94C THR* 1.3 66.3 + - + +
96C CYS* 2.8 7.7 + - + +
97C GLU* 2.7 43.6 + - - +
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Residues in contact with THR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C VAL* 3.0 38.7 - - + +
56C ASN 6.0 0.4 - - - +
90C LEU* 3.4 25.6 - - + +
91C CYS* 3.1 7.2 + - - -
93C LYS* 1.3 83.5 - - + +
95C VAL* 1.3 54.8 + - - +
97C GLU* 2.9 24.0 - - - +
98C CYS* 3.0 19.2 + - - -
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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
----------------------------------------------------------
1C ASN 5.2 0.9 - - - +
52C TYR* 3.7 23.3 - - + +
55C VAL* 4.2 9.4 - - + -
59C CYS* 5.0 0.4 - - - -
68C PRO* 4.0 39.3 - - + +
71C ALA* 4.5 10.1 - - + -
73C TYR* 3.5 21.8 - - + -
91C CYS 3.6 16.8 - - - +
92C LEU 2.8 7.8 + - - +
94C THR* 1.3 72.3 + - - +
96C CYS* 1.3 59.1 + - - +
97C GLU 2.7 9.9 + - - -
98C CYS* 4.2 5.4 - - - +
99C ASP* 2.9 31.5 + - - +
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Residues in contact with CYS 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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8C MET* 5.6 5.2 - - - +
73C TYR* 3.4 37.5 - - + -
74C SER 4.2 3.4 - - - -
75C TYR* 4.1 18.6 - - - -
82C ILE* 6.1 0.4 - - - -
83C VAL 4.2 0.2 - - - -
84C CYS* 2.0 54.1 - - + -
86C ASP* 4.7 0.9 - - + -
92C LEU 3.1 4.2 + - - -
93C LYS* 2.8 11.3 + - - +
95C VAL* 1.3 75.5 - - - +
97C GLU* 1.3 57.6 + - - +
99C ASP* 4.2 1.3 - - - +
100C ARG* 3.1 23.8 + - - +
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Residues in contact with GLU 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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51C CYS* 5.7 0.7 - - - -
84C CYS* 4.4 0.7 - - - +
93C LYS* 2.7 15.8 + - - +
94C THR* 2.9 22.4 - - - +
95C VAL 2.7 0.6 - - - -
96C CYS* 1.3 76.7 - - - +
98C CYS* 1.3 54.1 + - - +
100C ARG* 2.4 80.5 + - - +
101C ALA* 2.7 14.1 + - + +
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Residues in contact with CYS 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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48C HIS* 3.7 10.0 - - + +
51C CYS* 2.0 69.7 - - + -
52C TYR* 4.0 19.7 - - + -
55C VAL* 4.8 1.3 - - - -
94C THR* 3.0 18.1 + - - -
95C VAL* 3.1 4.5 + - - +
97C GLU* 1.3 77.5 - - - +
99C ASP* 1.3 56.8 + - - +
101C ALA* 2.8 27.0 + - - +
102C ALA* 2.9 13.5 + - - +
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Residues in contact with ASP 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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1C ASN 4.0 2.1 - - - +
5C PHE* 2.9 35.8 - - + +
8C MET* 4.1 11.1 - - + +
48C HIS* 3.2 14.2 + - - -
52C TYR* 3.0 25.4 + - - -
73C TYR* 2.5 35.8 + - + +
95C VAL* 2.9 16.3 + - - +
96C CYS 4.4 2.9 - - - +
98C CYS* 1.3 73.3 - - - +
100C ARG* 1.3 58.8 + - - +
102C ALA* 3.9 1.3 - - - +
103C ALA* 3.3 24.8 + - - +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C MET* 5.4 2.7 - - + -
81C ASP* 5.5 2.4 + - - -
82C ILE* 4.5 34.6 + - + +
83C VAL* 4.2 9.7 - - - +
84C CYS* 3.0 40.9 - - - +
96C CYS 3.1 10.6 + - - +
97C GLU* 2.4 69.6 + - - +
99C ASP* 1.3 74.3 - - - +
101C ALA* 1.3 60.3 + - + +
102C ALA 3.2 1.0 + - - -
103C ALA* 3.8 1.9 + - - +
104C ILE* 3.4 34.1 + - + +
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Residues in contact with ALA 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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47C VAL* 6.2 3.6 - - + -
51C CYS* 5.7 2.9 - - - -
97C GLU* 2.7 13.7 + - + +
98C CYS* 2.8 12.3 + - - +
100C ARG* 1.3 73.7 - - + +
102C ALA* 1.3 57.7 + - - +
104C ILE* 4.1 6.4 - - - +
105C CYS* 3.3 23.0 + - - +
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Residues in contact with ALA 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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5C PHE* 3.5 17.5 - - + -
44C CYS 5.1 6.5 - - - +
45C CYS* 6.3 0.4 - - - -
48C HIS* 3.2 36.3 - - + -
98C CYS 2.9 4.3 + - - +
99C ASP 4.0 0.2 - - - +
101C ALA* 1.3 77.1 - - - +
103C ALA* 1.3 60.4 + - - +
104C ILE 3.0 1.8 - - - -
105C CYS* 3.4 5.8 - - - +
106C LEU* 2.7 44.5 + - + +
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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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8C MET* 3.8 20.6 - - + +
9C ILE* 3.8 13.8 - - + +
12C MET* 3.2 43.3 - - + +
13C THR* 4.8 0.3 - - - +
82C ILE* 4.2 6.5 - - + -
99C ASP 3.3 16.4 + - - +
100C ARG 3.8 1.1 + - - +
102C ALA* 1.3 79.0 - - - +
104C ILE* 1.3 60.5 + - - +
106C LEU* 4.4 1.5 - - - +
107C GLY* 3.2 17.3 + - - -
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Residues in contact with ILE 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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12C MET* 4.4 18.2 - - + -
82C ILE* 5.4 3.1 - - + -
100C ARG* 3.4 29.7 + - + +
101C ALA* 4.2 6.7 - - - +
102C ALA 3.0 0.4 - - - -
103C ALA* 1.3 77.3 - - - +
105C CYS* 1.3 57.8 + - - +
107C GLY* 3.3 0.7 + - - -
108C GLN* 2.7 71.2 + - + +
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Residues in contact with CYS 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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40C ALA 4.5 1.1 - - - -
43C ARG 4.9 1.6 - - - -
44C CYS* 2.0 53.4 - - + +
47C VAL* 6.0 2.2 - - - -
101C ALA 3.3 19.1 + - - +
102C ALA* 2.9 6.2 + - - +
104C ILE* 1.3 82.2 - - - +
106C LEU* 1.3 64.7 + - - +
108C GLN* 3.0 6.0 + - - -
109C ASN* 2.7 31.3 + - - +
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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
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5C PHE* 4.7 4.9 - - + -
9C ILE* 3.3 44.4 - - + -
22C TYR* 3.7 49.7 + - + +
41C THR* 4.2 9.5 - - + +
44C CYS* 3.4 26.9 - - + -
45C CYS* 4.2 9.6 - - - -
102C ALA* 2.7 22.8 + - + +
103C ALA 4.4 2.2 - - - +
105C CYS* 1.3 75.1 - - - +
107C GLY* 1.3 64.4 - - - +
109C ASN* 3.2 9.4 + - - +
110C VAL* 3.5 16.7 + - - +
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Residues in contact with GLY 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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12C MET 4.8 0.2 - - - -
13C THR* 3.4 33.8 + - - +
103C ALA 3.2 11.5 + - - -
104C ILE 3.7 2.0 - - - -
105C CYS 3.2 0.8 - - - -
106C LEU* 1.3 79.5 - - - +
108C GLN* 1.3 57.4 - - - +
109C ASN 3.0 5.7 + - - -
110C VAL* 3.1 26.0 - - - +
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Residues in contact with GLN 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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104C ILE* 2.7 49.2 + - + +
105C CYS* 3.8 2.5 - - - +
107C GLY* 1.3 70.4 - - - +
109C ASN* 1.3 69.0 + - - +
110C VAL 3.8 0.9 - - - -
111C ASN* 3.8 10.3 + - - +
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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
------------------------------------------------------------
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