Contacts of the helix formed by residues 96 - 115 (chain A) in PDB entry 1H3N
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 HIS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ALA* 4.2 0.2 - - - -
95A VAL* 1.3 76.1 - - - +
97A PRO* 1.3 83.3 - - + +
98A LYS* 3.3 42.0 + - + +
99A ASP* 3.2 26.3 + - - +
100A TRP* 2.9 23.7 + - - +
429A TYR* 4.8 8.0 + + - -
430A TRP* 5.2 2.0 - - - -
458A ASP* 5.1 5.2 + - - -
459A LEU 3.0 28.9 + - - -
460A LYS* 4.2 16.7 + - + +
462A VAL* 3.9 18.0 - - + +
465A ILE* 4.8 4.8 - - + +
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Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA 5.3 0.4 - - - +
87A GLU* 4.7 6.3 - - + +
90A ALA* 3.7 16.2 - - + -
91A LEU* 4.6 1.3 - - + -
95A VAL 3.5 3.3 - - - +
96A HIS* 1.3 101.8 - - + +
98A LYS* 1.3 57.3 + - - +
100A TRP* 3.9 0.7 - - - +
101A THR* 2.8 36.9 + - - +
429A TYR* 4.4 3.1 - - + -
430A TRP* 3.6 44.6 - - + -
465A ILE* 3.3 30.1 - - + -
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Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A HIS* 3.3 20.7 - - + +
97A PRO* 1.3 80.9 - - - +
99A ASP* 1.3 66.7 + - - +
101A THR* 3.9 0.8 - - - -
102A TYR* 3.0 55.2 + - + +
430A TRP* 3.8 23.1 - - + -
458A ASP* 5.0 12.6 + - - +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.5 8.2 - - + +
96A HIS* 3.2 34.4 + - + +
98A LYS* 1.3 77.3 - - - +
100A TRP* 1.3 66.9 + - - +
101A THR 3.3 0.2 + - - -
102A TYR* 4.0 2.5 - - - +
103A ALA* 3.1 25.2 + - - +
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Residues in contact with TRP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO 3.6 20.7 + - - -
45A SER* 3.6 21.7 - - - +
46A GLY* 4.7 2.2 - - - -
86A ALA 4.0 6.3 - - - -
89A ALA* 3.8 22.8 - - + +
90A ALA* 3.6 26.0 - - + -
93A PHE* 3.5 39.7 - + + -
95A VAL* 3.8 26.6 - - + +
96A HIS 2.9 16.5 + - - +
97A PRO 3.9 0.7 - - - +
99A ASP* 1.3 77.8 - - - +
101A THR* 1.3 66.8 + - - +
103A ALA* 3.5 5.0 + - - +
104A ASN* 3.0 32.5 + - - +
640A LYS* 4.9 2.7 - - - -
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Residues in contact with THR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 3.8 11.8 - - + +
81A ALA* 3.6 31.0 - - + -
86A ALA* 4.0 19.6 + - - +
97A PRO 2.8 23.6 + - - -
98A LYS* 3.9 5.2 - - - -
99A ASP 3.3 0.2 - - - -
100A TRP* 1.3 81.0 - - - +
102A TYR* 1.3 63.1 + - + +
104A ASN* 3.1 4.3 + - - +
105A ILE* 2.8 42.6 + - + +
128A CYS* 4.3 8.5 - - - -
430A TRP* 4.0 7.8 + - - -
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LYS* 3.0 54.0 + - + +
99A ASP* 4.2 2.9 - - - +
101A THR* 1.3 78.4 - - + +
103A ALA* 1.3 64.1 + - - +
105A ILE* 3.6 15.4 - - + +
106A ARG* 3.1 23.2 + - - +
126A THR* 3.9 14.5 - - + +
128A CYS* 4.0 15.1 - - - -
129A GLU* 2.8 42.6 + - - +
430A TRP* 5.7 0.2 - + - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP 3.1 18.0 + - - +
100A TRP* 3.8 6.1 - - - +
102A TYR* 1.3 77.4 - - - +
104A ASN* 1.3 61.8 + - - +
106A ARG* 3.5 9.6 + - - +
107A GLN* 3.0 38.1 + - - +
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 3.1 28.5 - - - +
45A SER 4.2 1.2 - - - -
46A GLY* 2.5 57.2 + - - +
47A ASP* 4.2 1.4 + - - +
100A TRP* 3.0 27.3 + - - +
101A THR 3.4 4.9 - - - +
103A ALA* 1.3 76.5 - - - +
105A ILE* 1.3 58.8 + - - +
107A GLN* 3.3 16.1 + - - +
108A ALA* 2.9 31.3 + - - +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 4.0 10.1 - - + -
79A TRP* 3.6 57.6 - - + +
101A THR* 2.8 37.8 + - + +
102A TYR* 3.6 20.9 - - + +
103A ALA 3.3 0.2 - - - -
104A ASN* 1.3 77.0 - - - +
106A ARG* 1.3 62.7 + - - +
108A ALA* 3.2 8.0 + - - +
109A LYS* 3.0 35.5 + - - +
124A GLU* 4.5 1.3 - - - +
126A THR* 4.0 14.6 - - + +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR 3.1 17.1 + - - +
103A ALA* 3.6 9.2 - - - +
105A ILE* 1.3 78.0 - - - +
107A GLN* 1.3 64.8 + - + +
109A LYS* 3.5 10.0 + - - +
110A GLU* 3.3 20.8 + - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ASP* 2.8 33.1 - - - +
103A ALA* 3.0 30.9 + - - +
104A ASN* 3.6 13.3 + - - +
105A ILE 3.2 0.4 - - - -
106A ARG* 1.3 77.6 - - + +
108A ALA* 1.3 64.6 + - - +
110A GLU* 3.2 11.6 + - - +
111A SER* 3.1 26.3 + - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 5.6 0.4 - - + -
44A PRO* 6.3 1.1 - - + -
48A LEU* 3.9 29.6 - - + +
79A TRP* 3.5 28.7 - - + -
104A ASN* 2.9 19.8 + - - +
105A ILE* 3.2 2.2 + - - +
107A GLN* 1.3 76.0 - - - +
109A LYS* 1.3 62.4 + - - +
111A SER* 3.2 5.0 + - - -
112A LEU* 3.0 29.0 + - - +
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.6 15.7 - - + +
105A ILE* 3.0 27.3 + - + +
106A ARG* 3.7 9.4 - - - +
108A ALA* 1.3 76.2 - - - +
110A GLU* 1.3 58.1 + - - +
112A LEU* 3.3 9.2 + - - +
113A ARG* 2.9 31.1 + - - +
121A TRP* 3.9 26.1 - - + -
124A GLU* 3.0 40.6 + - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG 3.3 9.6 + - - +
107A GLN* 3.2 14.8 + - - +
109A LYS* 1.3 80.0 - - - +
111A SER* 1.3 56.5 + - - +
113A ARG* 3.2 7.4 + - - +
114A LEU* 2.8 59.6 + - + +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.5 22.0 + - - +
53A LEU* 4.5 1.9 - - - +
107A GLN* 3.1 14.3 + - - +
108A ALA* 3.2 11.5 + - - -
110A GLU* 1.3 76.8 - - - +
112A LEU* 1.3 62.6 + - - +
114A LEU* 4.6 2.2 - - - -
115A MET* 3.5 19.8 + - - +
648A VAL* 3.5 41.3 + - - +
649A GLY 5.0 2.6 + - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 6.3 0.2 - - + -
48A LEU* 4.3 11.4 - - + -
53A LEU* 4.5 4.7 - - + -
56A TYR* 3.8 28.5 - - + -
77A MET* 3.9 21.8 - - + -
79A TRP* 4.1 10.5 - - + -
108A ALA 3.0 21.7 + - - +
109A LYS* 3.7 3.6 - - - +
111A SER* 1.3 74.4 - - - +
113A ARG* 1.3 64.4 + - - +
115A MET* 3.2 10.2 + - - +
117A ILE* 3.2 42.2 + - + +
119A TYR* 3.9 29.8 - - + +
121A TRP* 4.0 14.1 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 4.7 1.8 + - - -
14A GLN* 3.1 56.4 + - + +
15A ARG* 3.3 45.5 - - - +
18A GLU* 4.0 19.6 + - - +
109A LYS 2.9 18.3 + - - +
110A GLU* 3.8 6.5 - - - +
112A LEU* 1.3 77.1 - - - +
114A LEU* 1.3 61.1 + - + +
116A GLY* 3.1 9.4 + - - -
117A ILE 4.4 8.3 - - - -
118A LEU* 5.8 2.2 - - - +
121A TRP* 6.0 2.6 - - + +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 4.8 0.7 - - - +
11A ALA* 6.5 0.4 - - + -
14A GLN* 3.2 25.5 + - - +
110A GLU* 2.8 54.5 + - + +
111A SER* 4.0 5.6 - - - +
112A LEU 3.3 0.4 - - - -
113A ARG* 1.3 75.4 - - + +
115A MET* 1.3 57.6 + - - +
116A GLY 3.3 1.1 - - - -
648A VAL* 4.2 9.2 - - + -
649A GLY* 4.4 14.6 - - - -
652A VAL* 4.1 28.3 - - + +
657A ALA* 3.3 12.5 - - - +
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A MET* 4.4 7.9 - - - -
53A LEU* 3.5 33.4 - - + -
57A THR* 3.9 15.0 - - - +
111A SER 3.5 13.8 + - - +
112A LEU 3.2 6.8 + - - +
113A ARG 3.1 1.0 - - - -
114A LEU* 1.3 76.7 - - - +
116A GLY* 1.3 58.7 + - - +
117A ILE* 3.2 5.4 - - + -
648A VAL* 3.7 13.0 - - + -
652A VAL* 4.0 15.5 - - - -
657A ALA* 3.9 10.8 - - - +
660A ALA* 3.7 34.3 - - + -
661A ARG* 3.0 52.9 + - + +
664A ILE* 4.5 2.2 - - + -
785A HIS* 3.9 0.7 - - - -
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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