Contacts of the helix formed by residues 103 - 117 (chain A) in PDB entry 1YH2
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.8 3.6 - - - +
10A GLU* 3.3 19.1 - - + +
61A TYR* 3.6 9.9 - - - -
66A PRO* 5.1 0.2 - - - -
98A TRP* 3.9 5.8 - - - -
101A SER 4.4 5.7 + - - -
102A LEU* 1.3 81.5 + - - +
104A ILE* 1.3 64.6 + - - +
105A ALA* 3.2 10.7 + - - +
106A THR* 2.9 46.3 + - - +
107A VAL* 3.0 23.4 + - - +
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Residues in contact with ILE 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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7A LEU* 4.4 10.5 - - + -
10A GLU* 2.8 31.9 + - + +
11A LEU* 5.9 0.9 - - + -
14A LEU* 3.9 22.7 - - + -
24A CYS* 4.0 8.7 - - - -
34A LEU* 3.9 15.0 - - + -
55A VAL* 4.4 10.1 - - + -
57A ILE* 3.7 32.3 - - + -
61A TYR* 3.6 7.5 + - - +
66A PRO* 4.1 5.2 - - + -
68A ILE* 5.6 0.4 - - + -
103A ASN* 1.3 72.4 - - - +
105A ALA* 1.3 62.4 + - - +
107A VAL* 3.3 9.4 + - + +
108A LEU* 3.0 42.7 + - + +
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Residues in contact with ALA 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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10A GLU* 4.5 1.0 + - - -
13A MET* 6.4 2.0 - - + -
14A LEU* 3.8 23.8 - - + +
17A GLU 6.0 0.7 - - - +
19A PRO* 4.1 20.1 - - + +
103A ASN* 3.2 10.3 + - - +
104A ILE* 1.3 79.7 - - - +
106A THR* 1.3 63.7 + - + +
108A LEU* 3.4 5.5 + - - +
109A THR* 2.8 29.6 + - - -
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Residues in contact with THR 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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101A SER 5.5 0.7 - - - +
102A LEU* 3.6 23.3 - - + +
103A ASN* 2.9 47.2 + - - +
105A ALA* 1.3 78.8 - - + +
107A VAL* 1.3 67.0 + - - +
109A THR* 3.3 7.9 + - - -
110A SER* 2.9 26.4 + - - -
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Residues in contact with VAL 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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66A PRO* 4.0 15.5 - - + -
68A ILE* 3.8 24.5 - - + -
87A LEU* 4.4 0.3 - - - +
89A VAL* 3.7 28.3 - - + +
90A LEU* 4.3 9.2 - - + -
98A TRP* 3.6 31.9 - - + -
102A LEU* 4.7 1.6 - - + -
103A ASN 3.0 13.8 + - - +
104A ILE 3.4 9.9 - - - +
106A THR* 1.3 80.6 - - - +
108A LEU* 1.3 60.1 + - - +
110A SER* 3.2 7.7 + - - -
111A ILE* 2.9 31.9 + - - +
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Residues in contact with LEU 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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14A LEU* 4.6 4.3 - - + -
22A ILE* 3.6 31.2 - - + +
24A CYS* 3.8 23.1 - - + -
36A ALA* 3.8 22.7 - - + -
38A ILE* 3.8 11.6 - - + +
53A LEU* 5.0 1.8 - - + -
55A VAL* 4.2 5.2 - - + -
68A ILE* 4.1 22.9 - - + -
104A ILE* 3.0 39.4 + - + +
105A ALA* 3.9 4.0 - - - +
107A VAL* 1.3 76.3 - - - +
109A THR* 1.3 56.4 + - - +
111A ILE* 3.3 14.4 + - + +
112A GLN* 2.9 28.4 + - - +
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Residues in contact with THR 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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19A PRO* 3.5 25.3 - - + +
22A ILE* 3.6 7.6 - - - +
105A ALA 2.8 22.5 + - - -
106A THR* 3.5 8.1 - - - -
108A LEU* 1.3 74.3 - - - +
110A SER* 1.3 58.7 + - - +
112A GLN* 3.3 13.7 + - - +
113A LEU* 2.9 29.5 + - + +
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Residues in contact with SER 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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87A LEU* 3.9 12.4 - - - +
88A ASP* 5.8 0.2 - - - -
89A VAL* 3.7 31.7 - - - +
106A THR* 2.9 15.4 + - - -
107A VAL 3.2 8.0 + - - -
109A THR* 1.3 77.0 - - - +
111A ILE* 1.3 58.5 + - - +
113A LEU* 3.3 9.2 + - - +
114A LEU* 2.8 27.9 + - - +
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Residues in contact with ILE 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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38A ILE* 3.7 16.8 - - + -
53A LEU* 4.2 4.0 - - + -
68A ILE* 3.6 42.2 - - + -
70A PHE* 3.7 27.4 - - + -
79A ILE* 5.6 0.4 - - + -
85A ILE* 3.9 16.6 - - + -
87A LEU* 3.5 20.9 - - + -
90A LEU* 4.4 4.9 - - + -
107A VAL 2.9 18.7 + - - +
108A LEU* 3.6 12.1 - - + +
110A SER* 1.3 73.4 - - - +
112A GLN* 1.3 69.0 + - - +
114A LEU* 3.1 7.8 + - + +
115A MET* 3.0 22.1 + - + +
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Residues in contact with GLN 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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19A PRO* 5.4 0.7 - - - +
20A PRO 3.0 25.1 + - - +
21A GLY* 3.9 10.3 + - - -
22A ILE* 3.7 22.6 - - + +
38A ILE* 4.0 17.2 - - + +
39A LEU 4.9 4.7 + - - +
108A LEU 2.9 14.0 + - - +
109A THR* 3.5 19.0 - - - +
111A ILE* 1.3 78.3 - - - +
113A LEU* 1.3 62.1 + - - +
115A MET* 3.2 24.0 + - - +
116A SER* 3.3 13.5 + - - +
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Residues in contact with LEU 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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109A THR* 2.9 18.2 + - + +
110A SER* 3.7 8.5 - - - +
112A GLN* 1.3 77.7 - - - +
114A LEU* 1.3 57.8 + - - +
116A SER* 3.1 10.6 + - - +
117A GLU* 2.7 60.6 + - + +
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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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76A HIS* 2.8 26.1 + - + +
78A ASN* 3.7 27.1 - - + +
79A ILE* 4.8 7.0 - - + -
85A ILE* 3.9 22.2 - - + -
86A CYS 3.9 18.2 - - - +
87A LEU* 4.2 18.4 - - + -
110A SER 2.8 14.3 + - - +
111A ILE* 3.1 11.6 + - + +
113A LEU* 1.3 75.8 - - - +
115A MET* 1.3 62.2 + - - +
117A GLU 3.2 25.6 + - - +
119A ASN* 3.6 23.3 - - - +
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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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38A ILE* 3.9 30.7 - - + -
39A LEU 4.5 0.7 - - - +
40A GLY* 4.3 11.4 - - - -
41A GLY 5.2 1.1 - - - +
44A THR* 5.1 1.0 - - - -
45A PRO* 5.9 0.2 - - - +
46A TYR* 3.2 33.9 - - + -
51A PHE* 3.7 36.3 - - + -
70A PHE* 4.0 21.5 - - + -
74A ILE* 4.0 21.5 - - + -
76A HIS* 3.7 13.2 + - + -
79A ILE* 4.9 2.7 - - + -
111A ILE* 3.0 19.1 + - + +
112A GLN* 3.4 8.3 - - - +
113A LEU 3.2 0.4 - - - -
114A LEU* 1.3 77.1 - - - +
116A SER* 1.3 60.0 + - - +
118A PRO* 4.2 4.2 - - - +
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Residues in contact with SER 116 (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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41A GLY* 5.3 4.5 - - - -
44A THR* 3.7 26.9 - - - +
112A GLN* 3.3 10.0 + - - +
113A LEU* 3.1 14.8 + - - -
115A MET* 1.3 80.2 - - - +
117A GLU* 1.3 70.1 + - - +
118A PRO* 3.6 6.9 - - - +
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Residues in contact with GLU 117 (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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113A LEU* 2.7 40.7 + - + +
114A LEU* 3.3 17.1 - - - +
116A SER* 1.3 85.8 - - - +
118A PRO* 1.3 71.1 - - - +
119A ASN* 3.8 6.2 + - - -
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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