Contacts of the helix formed by residues 100 - 114 (chain A) in PDB entry 4HFG
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 CYS 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.2 26.2 - - + -
92A VAL* 4.0 17.3 - - + -
93A ALA* 3.9 34.3 - - - -
96A ALA* 4.9 1.8 - - + -
97A ASP 4.2 14.6 - - - +
98A GLU* 3.5 2.0 + - - -
99A GLY* 1.3 79.5 - - - +
101A LYS* 1.3 63.5 + - - +
103A PRO* 3.3 7.1 - - - +
104A LEU* 2.9 35.4 + - + +
206A UNX 3.8 0.2 - - - -
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Residues in contact with LYS 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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93A ALA* 6.5 0.2 - - - -
99A GLY 3.4 1.6 - - - -
100A CYS* 1.3 81.9 - - - +
102A LYS* 1.3 58.6 + - - +
104A LEU* 3.2 5.2 + - - +
105A GLU* 2.8 45.3 + - - +
129A MET* 5.6 4.5 - - + -
206A UNX 3.6 16.3 - - - -
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Residues in contact with LYS 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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99A GLY 4.9 0.4 - - - -
101A LYS* 1.3 73.2 - - - +
103A PRO* 1.3 77.7 - - + +
105A GLU* 3.8 12.3 + - - +
106A ARG* 3.0 26.9 + - - +
28B LEU* 4.5 11.6 - - + +
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Residues in contact with PRO 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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57A LEU* 4.2 9.2 - - + -
61A TYR* 3.5 32.6 - - + +
99A GLY 3.0 28.0 - - - +
100A CYS* 3.3 8.7 - - - +
102A LYS* 1.3 96.1 - - + +
104A LEU* 1.3 58.2 + - - +
106A ARG* 3.6 3.7 - - + +
107A LEU* 3.0 29.6 + - - +
25B THR* 5.4 4.5 - - + +
28B LEU* 4.2 24.1 - - + +
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Residues in contact with LEU 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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57A LEU* 3.7 21.1 - - + -
60A LEU* 3.8 30.3 - - + -
89A PHE* 3.8 18.2 - - + +
92A VAL* 3.9 20.6 - - + -
93A ALA* 4.8 2.2 - - - +
100A CYS* 2.9 28.5 + - + +
101A LYS 3.8 1.6 - - - +
103A PRO* 1.3 73.9 - - - +
105A GLU* 1.3 66.2 + - - +
107A LEU* 3.5 19.0 + - + +
108A LEU* 3.1 29.1 + - - +
129A MET* 3.6 29.4 - - - -
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Residues in contact with GLU 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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101A LYS* 2.8 32.7 + - - +
102A LYS* 3.8 13.5 + - - +
104A LEU* 1.3 72.2 - - - +
106A ARG* 1.3 63.4 + - - +
108A LEU* 3.0 8.6 + - - +
109A ASN* 2.9 32.4 + - - +
126A LYS* 5.9 5.4 - - + -
129A MET* 4.1 19.2 - - + +
203A SO4 6.0 0.2 - - - +
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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 LYS 3.0 18.7 + - - +
103A PRO 3.6 3.8 - - - +
105A GLU* 1.3 75.7 - - - +
107A LEU* 1.3 58.3 + - - +
109A ASN* 3.2 3.6 + - - +
110A ILE* 2.9 41.9 + - + +
203A SO4 2.6 43.5 + - - +
28B LEU* 3.6 34.7 + - + +
31B ILE* 4.3 16.4 - - - +
69B ASN 5.6 1.2 + - - -
72B ARG* 3.5 18.2 - - - +
73B LYS* 3.6 10.4 - - - +
201B SO4 2.8 35.6 + - - -
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Residues in contact with LEU 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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60A LEU* 4.4 10.3 - - + +
61A TYR* 4.8 12.6 - - + -
64A ASN* 4.1 33.2 - - + +
89A PHE* 4.0 18.8 - - + -
103A PRO 3.0 17.6 + - - +
104A LEU* 3.6 22.4 - - + +
106A ARG* 1.3 78.8 - - - +
108A LEU* 1.3 61.8 + - + +
110A ILE* 3.5 8.0 + - - +
111A TRP* 3.0 58.5 + - + -
24B GLN* 5.1 0.2 - - - +
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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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89A PHE* 3.9 20.6 - - + -
104A LEU 3.1 17.4 + - - +
105A GLU* 3.0 8.8 + - - +
107A LEU* 1.3 75.9 - - + +
109A ASN* 1.3 61.1 + - - +
111A TRP* 3.2 19.4 + - + +
112A GLN* 2.9 29.5 + - - +
122A ILE* 3.8 19.0 - - + +
125A LEU* 3.6 33.9 - - + -
126A LYS* 3.8 43.3 - - + +
129A MET* 4.1 7.9 - - + -
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Residues in contact with ASN 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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105A GLU* 2.9 22.6 + - - +
106A ARG 3.6 6.3 - - - +
108A LEU* 1.3 77.3 - - - +
110A ILE* 1.3 58.7 + - - +
112A GLN* 3.5 12.2 + - - +
113A GLU* 3.0 35.0 + - - +
126A LYS* 5.9 2.9 - - - +
203A SO4 3.0 38.4 + - - +
72B ARG* 4.1 4.0 - - - +
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Residues in contact with ILE 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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68A GLN* 4.2 6.1 - - - +
106A ARG* 2.9 39.9 + - + +
107A LEU* 3.7 7.6 - - - +
109A ASN* 1.3 74.1 - - - +
111A TRP* 1.3 60.8 + - + +
113A GLU* 3.2 5.5 + - - +
114A ARG* 2.9 66.7 + - - +
208A UNX 3.7 12.1 - - - -
69B ASN* 3.8 27.4 - - + +
72B ARG* 3.7 29.6 - - - +
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Residues in contact with TRP 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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60A LEU* 5.6 0.4 - - + -
63A ALA* 5.5 1.8 - - + -
64A ASN* 2.9 43.5 + - + -
67A ILE* 4.0 16.2 - - + -
68A GLN* 4.3 8.8 - - - +
85A LEU* 4.0 20.2 - - + -
89A PHE* 4.3 10.5 - + - -
107A LEU* 3.0 33.8 + - + +
108A LEU* 3.2 26.2 + - + +
110A ILE* 1.3 75.8 - - + +
112A GLN* 1.3 58.7 + - - +
114A ARG 3.4 0.2 + - - -
115A SER* 2.9 8.7 + - - -
116A VAL* 2.8 56.8 + - + +
117A TYR* 3.9 24.5 + + - -
122A ILE* 3.4 12.3 - - + -
125A LEU* 3.8 22.4 - - + -
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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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108A LEU 2.9 15.7 + - - +
109A ASN* 3.6 12.4 + - - +
111A TRP* 1.3 76.3 - - - +
113A GLU* 1.3 64.5 + - + +
115A SER* 3.1 15.8 + - - +
117A TYR 4.9 3.3 - - - +
119A GLY* 3.1 32.3 + - - +
122A ILE* 4.0 24.0 - - + +
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Residues in contact with GLU 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 ASN* 3.0 19.2 + - - +
110A ILE* 3.2 5.9 + - - +
112A GLN* 1.3 80.0 - - + +
114A ARG* 1.3 64.8 + - + +
115A SER* 3.3 3.9 + - - -
72B ARG* 2.7 51.5 + - - +
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Residues in contact with ARG 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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68A GLN* 3.1 31.7 + - - +
71A LYS* 5.9 0.2 - - - -
110A ILE* 2.9 38.4 + - - +
113A GLU* 1.3 80.2 + - + +
115A SER* 1.3 70.9 + - - +
116A VAL* 3.1 13.5 + - + +
208A UNX 3.7 0.8 - - - -
68B GLN* 4.0 28.4 + - - +
69B ASN* 2.7 32.1 + - - +
72B ARG* 4.8 6.5 - - - +
114B ARG* 5.3 3.4 - - - +
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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