Contacts of the helix formed by residues 89 - 109 (chain D) 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 ASP 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D GLY 5.0 0.2 - - - -
88D ASP* 1.3 88.6 - - + +
90D PRO* 1.3 81.0 - - + +
91D CYS* 3.7 5.8 - - + +
92D LEU* 3.7 8.5 + - + +
93D ARG* 3.2 13.4 + - - +
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Residues in contact with PRO 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 1.3 95.0 - - + +
91D CYS* 1.3 60.6 - - - +
92D LEU 2.9 2.7 - - - -
93D ARG* 2.3 52.6 + - + +
94D ALA* 2.4 18.2 + - + -
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Residues in contact with CYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D VAL* 3.2 19.1 - - - +
56D LYS 2.7 31.8 + - - +
58D GLY* 4.8 0.2 - - - -
59D CYS* 2.0 57.1 - - + +
89D ASP* 3.7 5.7 - - + +
90D PRO* 1.3 77.3 - - - +
92D LEU* 1.3 59.5 + - + +
94D ALA* 4.0 2.6 - - - -
95D VAL* 2.9 32.1 + - - +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D CYS* 4.1 7.4 - - + -
71D VAL* 3.2 47.1 - - + -
72D GLU 4.6 5.6 - - - +
73D TYR* 3.9 27.9 - - + +
74D SER* 5.8 0.9 - - - +
88D ASP* 3.5 23.6 - - - +
89D ASP* 3.7 8.1 + - + +
90D PRO 2.5 5.6 + - - -
91D CYS* 1.3 77.1 - - + +
93D ARG* 1.3 54.6 + - - +
95D VAL* 2.9 3.8 + - - +
96D CYS* 2.7 37.6 + - - +
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Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D CYS* 4.2 13.9 - - - +
85D GLY* 5.5 1.8 - - - +
86D GLY 3.1 13.6 + - - +
88D ASP 2.9 28.8 + - - +
89D ASP 3.2 9.6 + - - +
90D PRO* 2.3 34.9 + - - +
92D LEU* 1.3 72.9 - - - +
94D ALA* 1.3 54.8 + - - +
96D CYS* 3.6 6.8 - - - +
97D GLU* 2.4 49.8 + - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D CYS* 4.5 0.3 - - - -
54D ARG 5.4 2.7 - - - +
55D VAL* 4.1 18.2 - - + -
90D PRO* 2.4 25.6 + - + +
91D CYS* 4.8 0.9 - - - +
93D ARG* 1.3 74.9 - - + +
95D VAL* 1.3 53.5 + - - +
97D GLU* 2.9 11.9 - - + +
98D CYS* 2.6 36.8 + - - -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D TYR* 3.8 12.6 - - + -
55D VAL* 3.7 23.6 - - + -
59D CYS* 4.1 8.3 - - - -
68D PRO* 4.0 26.9 - - + +
71D VAL* 4.2 5.6 - - + -
73D TYR* 3.5 18.8 - - + -
91D CYS 2.9 24.5 + - - +
92D LEU* 2.9 6.6 + - - +
94D ALA* 1.3 72.0 - - - +
96D CYS* 1.3 68.2 + - - +
97D GLU 2.6 5.5 + - - -
98D CYS* 2.6 19.6 + - - +
99D ASP* 2.7 22.2 + - - +
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Residues in contact with CYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.2 2.9 - - - +
73D TYR* 3.4 44.6 - - + -
74D SER 4.4 3.8 - - - +
75D TYR* 4.0 12.1 - - - -
84D CYS* 2.0 66.8 - - + -
92D LEU 2.7 20.2 + - - +
93D ARG* 3.6 5.6 - - - +
95D VAL* 1.3 74.2 - - - +
97D GLU* 1.3 49.0 + - - +
99D ASP* 3.5 1.6 - - - +
100D ARG* 2.7 24.8 + - - +
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D CYS* 5.0 1.1 - - - -
84D CYS* 2.7 34.6 - - - +
93D ARG* 2.4 46.6 + - - +
94D ALA* 2.9 18.7 + - + +
95D VAL 2.6 1.0 + - - -
96D CYS* 1.3 75.5 - - - +
98D CYS* 1.3 57.7 + - - +
99D ASP 2.8 1.1 - - - -
100D ARG* 2.6 33.3 + - - +
101D VAL* 2.8 27.8 + - + +
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Residues in contact with CYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D HIS* 3.0 23.5 - - + +
51D CYS* 2.0 70.0 - - + -
52D TYR* 3.3 24.9 - - + -
55D VAL* 4.3 7.2 - - - -
94D ALA* 2.6 20.1 + - - -
95D VAL* 2.6 8.1 + - - +
97D GLU* 1.3 71.9 - - - +
99D ASP* 1.3 56.2 + - - +
101D VAL* 4.9 1.7 - - - +
102D ALA* 3.0 14.9 + - - +
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ASN 4.6 2.8 - - - +
5D PHE* 3.5 29.2 - - + +
8D LEU* 3.1 12.1 - - + +
48D HIS* 2.5 32.4 + - - -
52D TYR* 2.6 22.4 + - - -
68D PRO 5.1 0.3 - - - +
73D TYR* 3.0 42.3 + - - +
95D VAL* 2.7 16.3 + - - +
96D CYS 3.9 0.9 - - - +
98D CYS* 1.3 77.6 - - - +
100D ARG* 1.3 59.6 + - - +
102D ALA 4.2 2.0 - - - -
103D ALA* 3.7 13.5 - - - +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.9 8.3 - - + -
81D LYS* 3.7 29.2 - - - +
82D ILE* 3.0 41.8 + - + +
84D CYS* 3.5 16.6 - - - +
96D CYS 2.7 18.2 + - - +
97D GLU* 2.6 25.2 + - - +
99D ASP* 1.3 71.5 - - - +
101D VAL* 1.3 78.3 + - + +
102D ALA 3.3 0.4 - - - -
103D ALA* 3.4 13.7 + - - +
104D ILE* 2.9 29.5 + - + +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 6.4 1.8 - - + -
97D GLU* 2.8 23.5 + - + +
98D CYS* 4.9 1.6 - - - +
100D ARG* 1.3 91.8 - - - +
102D ALA* 1.3 66.4 + - - +
103D ALA 3.0 3.2 + - - -
104D ILE* 3.2 12.6 + - + +
105D CYS* 3.3 21.6 + - + +
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 3.6 14.8 - - + -
44D CYS* 4.2 7.2 - - - +
48D HIS* 3.3 29.4 - - + -
98D CYS 3.0 23.4 + - - +
99D ASP* 4.4 0.2 - - - -
100D ARG 3.3 0.6 - - - -
101D VAL* 1.3 79.9 - - - +
103D ALA* 1.3 59.8 + - - +
105D CYS* 3.3 16.0 - - - +
106D PHE* 3.1 23.8 - - + -
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 4.6 0.2 - - - -
8D LEU* 3.9 29.6 - - + +
9D ILE* 4.0 8.7 - - + +
12D LYS* 4.0 10.9 - - + +
13D GLN* 4.1 3.1 + - - -
82D ILE* 4.6 2.2 - - + -
99D ASP 3.7 12.5 + - - +
100D ARG 3.4 11.4 + - - +
101D VAL 3.0 0.2 - - - -
102D ALA* 1.3 76.6 - - - +
104D ILE* 1.3 58.9 + - - +
105D CYS 2.9 1.6 - - - -
106D PHE* 2.7 32.3 + - - +
107D ARG 3.2 9.0 + - - -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 4.2 30.9 - - + +
100D ARG* 2.9 44.9 - - + +
101D VAL* 3.2 26.7 - - + +
103D ALA* 1.3 75.7 - - - +
105D CYS* 1.3 61.4 + - - +
106D PHE 3.2 0.7 + - - -
107D ARG* 3.4 8.5 + - + +
108D GLU* 3.0 42.0 + - + +
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Residues in contact with CYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA 4.5 0.4 - - - -
43D ARG* 5.7 0.7 - - - -
44D CYS* 2.0 66.1 - - + -
101D VAL* 3.3 13.9 + - + +
102D ALA* 3.3 14.1 - - - +
104D ILE* 1.3 79.9 - - - +
106D PHE* 1.3 59.3 + - - +
108D GLU* 4.1 4.0 + - - +
109D ASN* 3.0 25.8 + - - +
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Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C TRP* 6.2 0.4 - + - -
5D PHE* 4.1 21.8 - + - -
9D ILE* 4.4 13.0 - - + -
13D GLN* 3.2 20.6 - - - +
22D TYR* 3.9 34.8 + + + +
29D CYS* 4.1 0.7 - - - -
41D THR* 3.4 29.5 + - + -
44D CYS* 3.3 27.8 - - + -
45D CYS* 3.2 29.4 - - - -
102D ALA* 3.1 21.5 - - + -
103D ALA* 2.7 15.6 + - - +
105D CYS* 1.3 70.7 - - - +
107D ARG* 1.3 62.2 + - - +
108D GLU 3.1 2.2 - - - -
109D ASN* 3.9 1.1 - - - -
110D MET* 3.1 26.5 + - - +
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 2.4 67.6 + - + +
13D GLN* 3.3 20.9 - - + +
14D GLU* 5.0 1.2 - - - +
103D ALA 3.2 3.4 + - - -
104D ILE* 3.4 7.6 + - - +
106D PHE* 1.3 78.0 - - - +
108D GLU* 1.3 76.0 + - - +
110D MET* 3.3 18.9 - - + +
111D ASN* 5.4 0.7 + - - -
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Residues in contact with GLU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ILE* 3.0 35.4 - - + +
105D CYS* 4.3 5.2 - - - +
106D PHE 3.1 0.8 - - - -
107D ARG* 1.3 88.8 - - - +
109D ASN* 1.3 61.2 + - - +
110D MET 2.7 15.1 + - - -
111D ASN* 3.6 12.6 + - - +
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Residues in contact with ASN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA* 3.3 37.1 + - + +
41D THR* 3.8 12.7 + - - +
44D CYS* 3.4 15.6 - - - -
105D CYS* 3.0 28.4 + - - +
106D PHE 3.9 1.3 - - - +
108D GLU* 1.3 74.2 - - - +
110D MET* 1.3 55.3 + - - +
111D ASN 3.0 6.3 - - - -
112D THR* 2.8 35.9 + - + +
113D TYR 3.4 2.9 + - - -
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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
------------------------------------------------------------
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