Contacts of the helix formed by residues 104 - 119 (chain A) in PDB entry 7A62
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 PRO 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 4.4 16.8 - - + +
60A GLU* 4.3 15.9 - - + +
90A TYR* 3.5 35.4 - - + +
102A VAL* 3.3 9.6 - - + +
103A LEU* 1.3 92.6 - - + +
105A ARG* 1.3 67.1 + - - +
106A ASN* 3.1 6.3 + - + +
107A ILE* 3.1 6.9 + - + +
108A ALA 2.8 19.9 + - - -
250A GLU* 3.8 9.6 - - - +
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Residues in contact with ARG 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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64A MET* 3.4 24.5 - - + +
103A LEU 3.6 0.4 + - - -
104A PRO* 1.3 72.4 - - - +
106A ASN* 1.3 67.5 + - - +
109A VAL* 3.1 31.6 + - + -
250A GLU* 3.1 47.9 + - - +
251A GLY* 3.2 25.0 + - - -
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Residues in contact with ASN 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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39A TRP* 4.9 2.9 + - - -
59A VAL 5.6 1.6 - - - +
60A GLU 5.5 0.8 + - - -
62A LEU* 2.6 36.1 + - + +
63A ASN* 3.5 8.5 + - - +
64A MET* 3.1 51.7 - - - +
65A LEU 4.6 0.9 + - - -
104A PRO* 3.1 5.2 + - + +
105A ARG* 1.3 83.3 - - - +
107A ILE* 1.3 62.4 + - + +
110A PRO* 3.3 17.3 - - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 4.2 9.4 - - + +
59A VAL* 4.1 17.9 - - + +
62A LEU* 3.7 32.8 - - + -
83A LEU* 3.8 28.8 - - + +
86A ILE* 4.4 16.6 - - + -
87A THR* 4.0 19.7 - - - +
103A LEU* 4.0 18.8 - - + -
104A PRO* 3.1 8.6 + - + +
106A ASN* 1.3 78.6 - - - +
108A ALA* 1.3 65.8 + - - +
109A VAL 3.3 1.6 - - - -
110A PRO* 3.3 4.4 - - - +
111A TYR* 2.9 28.0 + - + +
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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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103A LEU* 3.5 34.3 - - + +
104A PRO 2.8 16.5 + - - +
107A ILE* 1.3 78.0 - - - +
109A VAL* 1.3 57.4 + - - +
111A TYR* 3.8 1.7 - - - -
112A CYS* 2.9 36.3 + - - -
249A TYR* 3.8 9.4 - - + -
250A GLU 3.6 21.3 - - - +
252A PHE* 5.0 0.9 - - - -
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Residues in contact with VAL 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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64A MET* 4.0 15.9 - - + -
105A ARG* 3.1 25.4 + - + +
108A ALA* 1.3 75.7 - - - +
110A PRO* 1.3 71.9 - - + +
112A CYS* 3.2 2.9 + - - +
113A GLN* 2.9 51.1 + - + +
250A GLU 3.8 3.8 - - - +
251A GLY 3.6 33.0 - - - +
252A PHE* 4.2 12.5 - - + +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 4.1 14.8 - - + -
64A MET* 4.3 8.7 - - + -
65A LEU 3.7 24.7 - - - +
66A SER* 5.6 0.4 - - - -
67A ILE* 3.7 16.9 - - + +
83A LEU* 4.4 2.2 - - + -
105A ARG 3.8 2.5 - - - +
106A ASN 3.3 25.1 - - - +
107A ILE* 3.3 10.1 - - - +
109A VAL* 1.3 95.1 - - + +
111A TYR* 1.3 54.3 + - - +
113A GLN* 3.7 12.8 - - - +
114A LEU* 3.0 31.0 + - - +
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Residues in contact with TYR 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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80A ARG* 4.1 20.6 + - + -
83A LEU* 3.7 29.3 - - + +
84A GLY* 3.4 24.7 - - - -
87A THR* 3.5 31.4 - - + -
103A LEU* 4.3 11.0 - - + -
107A ILE* 2.9 22.2 + - + +
108A ALA 3.9 2.5 - - - +
110A PRO* 1.3 76.7 - - - +
112A CYS* 1.3 58.5 + - - +
114A LEU* 3.6 1.9 + - + +
115A SER* 2.7 45.4 + - - -
122A PRO* 3.4 30.1 - - + -
123A ILE* 3.0 31.7 + - - -
124A LEU* 4.2 0.2 - - - -
249A TYR* 4.8 0.9 - + - -
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Residues in contact with CYS 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 ALA 2.9 24.2 + - - +
109A VAL 3.7 0.9 - - - +
111A TYR* 1.3 76.3 - - - +
113A GLN* 1.3 64.8 + - - +
115A SER* 3.5 5.5 + - - -
116A ALA* 3.0 24.4 + - - +
122A PRO* 3.9 12.1 - - - -
249A TYR* 3.7 34.3 - - - -
252A PHE* 3.5 43.4 - - + -
253A TRP* 4.0 6.5 - - + -
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Residues in contact with GLN 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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66A SER* 5.7 1.6 - - - -
67A ILE* 3.6 29.3 + - + +
109A VAL* 2.9 37.7 + - - +
110A PRO* 3.3 12.3 + - - +
112A CYS* 1.3 77.5 - - - +
114A LEU* 1.3 61.3 + - - +
116A ALA* 3.2 7.5 + - - +
117A ALA* 3.0 21.7 + - - +
252A PHE* 4.2 16.4 - - + -
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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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67A ILE* 4.4 13.6 - - + +
70A LEU* 4.1 14.4 - - + -
76A GLN* 3.8 39.5 - - + +
79A ALA* 3.6 16.8 - - + -
80A ARG* 3.6 39.9 - - + +
83A LEU* 4.2 12.8 - - + -
110A PRO 3.0 16.4 + - - +
111A TYR* 3.9 4.0 - - + +
113A GLN* 1.3 77.4 - - - +
115A SER* 1.3 61.7 + - - +
117A ALA* 3.1 7.3 + - + +
118A LEU* 2.9 23.0 + - + +
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Residues in contact with SER 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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80A ARG* 2.9 25.5 + - - +
111A TYR* 2.7 28.1 + - - -
112A CYS 3.8 4.0 - - - -
114A LEU* 1.3 76.9 - - - +
116A ALA* 1.3 57.9 + - - +
118A LEU* 3.2 3.8 + - - +
119A GLU* 2.7 26.0 + - - -
120A LEU 3.1 28.1 + - - +
122A PRO* 3.6 21.4 - - - +
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Residues in contact with ALA 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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112A CYS 3.0 17.4 + - - +
113A GLN* 3.6 7.0 - - - +
114A LEU 3.2 0.2 - - - -
115A SER* 1.3 78.7 - - - +
117A ALA* 1.3 61.8 + - - +
118A LEU 3.5 0.3 + - - -
119A GLU* 3.5 15.0 + - - +
120A LEU 5.0 0.4 - - - -
252A PHE* 5.5 6.5 - - + -
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Residues in contact with ALA 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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67A ILE* 6.4 1.8 - - + -
76A GLN* 4.5 17.9 - - - +
113A GLN 3.0 13.2 + - - +
114A LEU* 3.1 10.5 + - - +
116A ALA* 1.3 78.5 - - - +
118A LEU* 1.3 62.7 + - - +
119A GLU* 3.8 7.1 + - - +
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Residues in contact with LEU 118 (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 HIS* 3.9 25.4 - - + +
76A GLN* 3.7 53.6 - - + +
77A ARG* 4.2 10.5 - - - -
80A ARG* 3.6 32.5 - - + -
114A LEU* 2.9 17.4 + - + +
115A SER 4.1 2.0 - - - +
117A ALA* 1.3 78.4 - - - +
119A GLU* 1.3 71.9 + - - +
120A LEU* 3.3 9.3 + - + +
301A PRO* 3.3 19.2 - - - +
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Residues in contact with GLU 119 (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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115A SER 2.7 12.8 + - - -
116A ALA* 3.5 12.9 + - - +
117A ALA 3.4 7.3 - - - +
118A LEU* 1.3 78.7 - - - +
120A LEU* 1.3 56.4 + - - +
297A ARG 4.6 0.5 - - - +
301A PRO* 3.8 22.8 - - + +
304A ARG* 2.8 45.2 + - - +
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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