Contacts of the helix formed by residues 103 - 115 (chain A) in PDB entry 2PHA
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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.7 31.6 - - + +
15A PHE* 3.7 32.3 - - + -
55A PHE* 4.1 13.0 - - + -
73A VAL 5.7 0.2 - - - +
76A ALA* 4.1 26.9 - - + +
77A SER* 3.7 5.6 - - - +
80A LEU* 2.9 34.6 - - + +
99A GLY 3.7 10.1 - - - +
100A ASP 3.5 15.3 - - - +
102A SER* 1.3 79.2 + - - +
104A ALA* 1.3 62.4 + - - +
105A ILE 3.2 0.4 - - - -
106A GLY 3.3 2.6 + - - -
107A SER* 3.0 7.4 + - - -
276A MET* 3.5 18.2 - - + -
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Residues in contact with ALA 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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101A HIS* 3.2 27.6 + - + +
102A SER 3.0 0.6 - - - -
103A LEU* 1.3 76.7 - - - +
105A ILE* 1.3 60.4 + - - +
107A SER* 3.0 8.0 + - - -
108A ILE* 2.8 35.8 + - + +
122A TRP* 3.6 32.5 - - + -
144A PRO* 4.2 2.2 - - + -
148A LEU* 4.4 2.2 - - + -
230A SER* 4.1 4.7 - - - +
274A ASP* 4.8 4.9 - - - +
276A MET* 4.7 1.8 - - - +
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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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73A VAL* 5.3 0.4 - - + -
77A SER* 3.7 5.2 - - - +
102A SER* 3.2 20.0 - - - +
104A ALA* 1.3 79.2 - - - +
106A GLY* 1.3 55.4 + - - +
109A SER* 2.5 34.6 + - - +
140A LEU* 5.1 4.5 - - + +
144A PRO* 3.5 26.9 - - + +
147A PHE* 3.8 39.3 - - + -
148A LEU* 3.4 19.5 - - + +
162A PHE* 3.9 19.5 - - + -
164A TRP* 4.2 6.7 - - + -
165A VAL* 4.3 22.0 - - + -
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Residues in contact with GLY 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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77A SER* 3.2 36.5 + - - -
80A LEU* 4.2 1.3 - - - -
81A ALA* 3.0 21.9 - - - +
103A LEU 3.3 3.5 + - - -
104A ALA 3.1 0.2 - - - -
105A ILE* 1.3 79.0 - - - +
107A SER* 1.3 59.7 + - - +
110A GLY* 2.8 23.4 + - - -
164A TRP* 4.0 3.4 - - - -
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Residues in contact with SER 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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80A LEU* 3.8 12.0 - - - +
84A VAL* 3.6 13.3 - - - +
94A SER* 5.5 1.0 + - - -
96A VAL* 3.9 9.2 - - - +
103A LEU 3.0 16.4 + - - -
104A ALA* 3.0 6.3 + - - -
106A GLY* 1.3 74.4 - - - +
108A ILE* 1.3 63.7 + - - +
111A HIS* 3.0 24.6 + - - +
228A HIS* 3.3 10.8 - - - -
274A ASP* 2.7 34.4 + - - -
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Residues in contact with ILE 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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104A ALA* 2.8 20.6 + - + +
107A SER* 1.3 72.6 - - - +
109A SER* 1.3 54.2 + - - +
111A HIS* 3.3 3.2 + - - +
112A ALA* 2.7 32.4 + - - +
118A LEU* 4.3 8.5 - - + -
120A VAL* 3.8 32.3 - - + -
122A TRP* 4.0 14.4 - - + -
148A LEU* 3.5 25.6 - - + -
168A CYS* 3.7 6.7 - - - -
169A ILE* 3.6 31.6 - - + -
174A ILE* 5.6 2.0 - - + -
228A HIS* 3.5 25.6 - - + +
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Residues in contact with SER 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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81A ALA* 4.6 1.1 - - - -
105A ILE* 2.5 26.0 + - - +
106A GLY 3.9 2.9 - - - -
107A SER 3.3 0.2 - - - -
108A ILE* 1.3 79.7 - - - +
110A GLY* 1.3 62.7 + - - +
112A ALA* 3.2 2.8 + - - +
113A ARG* 3.0 32.3 + - - +
148A LEU* 3.4 12.0 - - - +
164A TRP* 4.1 22.7 - - - -
165A VAL* 4.8 5.9 - - - +
166A THR 4.9 4.4 + - - -
168A CYS* 3.9 13.6 - - - +
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Residues in contact with GLY 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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81A ALA* 3.1 30.2 - - - +
84A VAL* 3.8 7.0 - - - -
85A ALA* 3.5 19.8 - - - +
106A GLY 2.8 18.8 + - - -
107A SER 4.0 0.9 - - - -
109A SER* 1.3 74.1 - - - +
111A HIS* 1.3 61.7 + - - +
113A ARG* 3.5 15.7 + - - +
114A VAL* 3.9 1.7 - - - +
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Residues in contact with HIS 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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84A VAL* 3.4 10.9 - - + +
88A LYS* 3.9 17.0 - - + -
94A SER* 4.9 0.4 + - - +
107A SER 3.0 18.9 + - - +
108A ILE 3.5 4.7 - - - +
110A GLY* 1.3 77.0 - - - +
112A ALA* 1.3 57.2 + - - +
114A VAL* 3.2 3.8 + - - +
115A HIS* 2.8 47.3 + - + +
118A LEU* 3.7 11.6 - - + +
226A PRO* 4.5 1.2 - - - +
227A ILE 4.4 1.3 - - - -
228A HIS* 3.2 31.1 + - + +
271A SER* 3.3 25.6 + - - -
272A GLY* 3.2 32.3 - - - -
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Residues in contact with ALA 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 ILE 2.7 20.9 + - - +
109A SER 3.2 4.7 + - - +
111A HIS* 1.3 70.7 - - - +
113A ARG* 1.3 63.1 + - - +
115A HIS 3.5 5.4 - - - +
116A PRO* 2.8 37.5 - - + +
118A LEU* 3.5 17.2 - - + +
168A CYS* 3.7 30.1 - - + +
169A ILE* 5.2 1.3 - - + -
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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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78A GLU* 4.9 6.9 + - - +
81A ALA* 3.8 12.8 + - - +
82A GLY* 4.0 24.7 - - - +
85A ALA* 4.6 7.6 - - + +
109A SER* 3.0 23.8 + - - +
110A GLY* 3.6 12.3 - - - +
111A HIS 3.2 0.4 - - - -
112A ALA* 1.3 77.2 - - - +
114A VAL* 1.3 63.5 + - + +
116A PRO* 4.4 3.3 - - - +
164A TRP* 3.8 32.7 + - - -
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Residues in contact with VAL 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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85A ALA* 3.6 39.9 - - + +
88A LYS* 4.1 8.3 - - + +
89A LYS* 4.0 28.0 - - + +
110A GLY 3.9 4.5 - - - +
111A HIS 3.2 2.6 + - - +
113A ARG* 1.3 80.6 - - + +
115A HIS* 1.3 89.4 + - + +
116A PRO* 3.6 6.5 - - - +
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Residues in contact with HIS 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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88A LYS* 3.4 33.8 + - + +
111A HIS* 2.8 31.1 + + + +
112A ALA* 3.2 8.5 - - - -
114A VAL* 1.3 108.4 + - + +
116A PRO* 1.3 59.3 - - - +
117A ASP* 3.0 21.8 + - - +
118A LEU* 3.1 17.5 + - - +
226A PRO* 4.1 24.2 - - + -
271A SER* 5.8 0.9 - - - -
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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
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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