Contacts of the helix formed by residues 106 - 124 (chain A) in PDB entry 3CP5
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 SER 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.6 5.6 - - - +
104A ALA 3.8 1.0 + - - -
105A LEU* 1.3 75.2 - - - +
107A GLU* 1.3 65.9 + - - +
108A GLU* 3.4 8.0 + - - +
109A GLN* 2.8 35.3 + - - +
110A ALA 3.0 17.2 + - - -
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Residues in contact with GLU 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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20A VAL* 4.7 9.4 - - + -
73A MET* 3.8 14.8 - - + +
77A LEU* 3.9 19.2 - - + +
106A SER* 1.3 74.0 - - - +
108A GLU* 1.3 70.3 + - - +
110A ALA* 3.2 1.6 + - - +
111A ARG* 2.8 43.8 + - - +
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Residues in contact with GLU 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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33A LEU* 3.7 14.1 - - + +
36A GLN* 2.7 40.9 + - - +
106A SER* 3.2 7.2 + - - +
107A GLU* 1.3 88.0 + - - +
109A GLN* 1.3 68.8 + - - +
111A ARG* 3.3 5.5 + - + +
112A ALA* 3.1 16.1 + - - +
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Residues in contact with GLN 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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36A GLN* 5.4 1.6 - - - +
40A LEU* 3.7 26.7 - - + +
44A TYR* 3.0 34.6 + - - -
104A ALA 4.1 3.1 - - - +
105A LEU* 3.5 19.0 - - + -
106A SER* 2.8 42.4 + - - +
108A GLU* 1.3 83.6 - - - +
110A ALA* 1.3 62.7 + - - +
112A ALA* 3.2 4.5 + - - +
113A ILE* 3.1 28.0 + - + +
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Residues in contact with ALA 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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73A MET* 3.6 14.6 - - + -
76A MET* 3.4 33.3 - - + +
77A LEU* 3.9 26.0 - - + -
105A LEU* 5.1 2.9 - - + +
106A SER 3.0 13.1 + - - +
107A GLU 3.7 6.5 - - - +
109A GLN* 1.3 78.1 - - - +
111A ARG* 1.3 55.3 + - - +
113A ILE* 3.2 2.6 + - - -
114A LEU* 2.9 26.9 + - - +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.7 6.5 - - - +
24A SER 2.8 31.1 + - - +
25A LEU* 3.4 28.4 - - - +
26A GLY 4.8 1.0 - - - +
33A LEU* 4.1 15.8 - - + +
73A MET* 3.7 13.6 - - + -
107A GLU* 2.8 32.7 + - - +
108A GLU* 3.7 8.1 - - + +
109A GLN 3.2 0.2 - - - -
110A ALA* 1.3 76.8 - - - +
112A ALA* 1.3 60.0 + - - +
114A LEU* 3.3 17.6 + - - +
115A GLU* 2.8 47.4 + - - +
118A ARG* 4.5 0.2 - - - +
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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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33A LEU* 3.6 25.7 - - + +
36A GLN* 3.5 31.9 - - - +
37A GLY* 3.3 14.0 - - - +
40A LEU* 3.9 3.8 - - + -
108A GLU 3.1 11.6 + - - +
109A GLN 3.6 7.9 - - - +
111A ARG* 1.3 73.7 - - - +
113A ILE* 1.3 65.2 + - - +
115A GLU* 3.1 5.0 + - - +
116A TYR 3.0 18.7 + - - -
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Residues in contact with ILE 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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37A GLY* 3.9 10.8 - - - +
40A LEU* 3.6 32.5 - - + +
41A PHE* 4.2 17.5 - - + +
44A TYR* 5.0 0.7 - - + -
45A CYS* 4.2 5.6 - - - -
76A MET* 3.7 21.5 - - + -
105A LEU* 4.7 10.8 - - + -
109A GLN 3.1 17.6 + - - +
110A ALA 3.2 6.0 + - - +
112A ALA* 1.3 74.5 - - - +
114A LEU* 1.3 57.0 + - - +
116A TYR* 3.1 3.9 + - - +
117A LEU* 2.9 30.5 + - + +
202A HEC 3.8 40.4 - - + -
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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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23A VAL* 4.7 2.0 - - + -
25A LEU* 4.6 9.4 - - + -
64A THR* 4.1 18.6 - - + -
69A PRO* 3.8 28.3 - - + +
72A ILE* 4.0 28.5 - - + -
73A MET* 4.2 20.0 - - + -
76A MET* 4.1 5.8 - - + +
110A ALA 2.9 13.5 + - - +
111A ARG* 3.5 31.6 - - - +
112A ALA 3.2 0.2 - - - -
113A ILE* 1.3 76.5 - - - +
115A GLU* 1.3 56.8 + - - +
117A LEU* 3.1 7.6 + - + +
118A ARG* 2.9 34.1 + - + +
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Residues in contact with GLU 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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26A GLY 5.5 1.4 + - - -
28A GLN 4.3 1.2 - - - +
29A ILE* 4.1 7.8 - - + +
30A ASP* 2.8 35.1 + - - +
33A LEU* 3.8 21.5 - - + +
34A ALA* 3.9 16.2 - - - +
111A ARG* 2.8 43.1 + - - +
112A ALA 3.1 8.7 + - - +
114A LEU* 1.3 75.9 - - - +
116A TYR* 1.3 61.0 + - - +
118A ARG* 3.0 37.6 + - - +
119A GLN* 3.0 21.8 + - - +
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Residues in contact with TYR 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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34A ALA* 3.6 22.1 - - + +
37A GLY* 3.6 11.9 - - - -
38A GLU* 3.5 42.8 + - + +
41A PHE* 3.7 49.6 - + + -
51A LEU* 3.8 17.0 - - + +
112A ALA 3.0 5.9 + - - -
113A ILE 3.4 8.5 - - - +
115A GLU* 1.3 75.5 - - - +
117A LEU* 1.3 61.0 + - + +
119A GLN* 3.0 9.8 + - + +
120A VAL* 2.9 54.0 + - + +
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Residues in contact with LEU 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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41A PHE* 4.1 22.7 - - + -
51A LEU* 4.8 2.5 - - + -
60A LEU* 4.1 27.6 - - + +
61A ARG 4.3 1.9 - - - +
63A VAL* 4.0 15.9 - - + -
64A THR* 3.7 16.7 + - + -
72A ILE* 4.1 20.6 - - + -
113A ILE* 2.9 32.2 + - + +
114A LEU* 3.1 9.4 + - - +
116A TYR* 1.3 78.9 - - + +
118A ARG* 1.3 59.4 + - - +
120A VAL* 3.4 14.3 - - + +
121A ALA* 3.2 22.9 + - - +
202A HEC 4.4 10.8 - - + -
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Residues in contact with ARG 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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25A LEU* 3.3 42.2 - - - +
26A GLY 4.1 16.4 + - - +
27A GLU 4.9 3.8 + - - -
28A GLN 4.4 4.2 + - - -
29A ILE* 3.8 29.0 - - + +
64A THR* 4.0 20.9 - - + -
111A ARG* 4.5 0.8 - - - +
114A LEU* 2.9 25.0 + - + +
115A GLU* 3.0 43.3 + - - +
117A LEU* 1.3 74.0 - - - +
119A GLN* 1.3 61.8 + - - +
121A ALA* 3.5 4.9 + - - +
122A GLU* 3.3 24.3 + - - +
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Residues in contact with GLN 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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29A ILE* 3.3 32.0 - - + +
31A ALA* 5.5 2.9 - - - +
34A ALA* 4.2 15.3 - - + +
115A GLU 3.0 12.7 + - - +
116A TYR* 3.0 13.7 + - + +
118A ARG* 1.3 75.0 - - - +
120A VAL* 1.3 65.4 + - + +
122A GLU* 3.0 13.2 + - - +
123A ASN* 2.9 52.9 + - - +
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Residues in contact with VAL 120 (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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51A LEU* 3.9 26.2 - - + -
61A ARG* 3.0 48.6 + - + +
116A TYR* 2.9 54.0 + - + +
117A LEU* 3.4 21.1 - - + +
119A GLN* 1.3 76.0 - - + +
121A ALA* 1.3 63.6 + - - +
123A ASN* 3.3 20.5 + - - +
124A GLN 3.4 2.6 + - - -
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Residues in contact with ALA 121 (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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61A ARG 3.5 17.5 - - - +
62A ASP* 4.2 6.4 - - - +
64A THR* 3.5 24.7 - - - +
65A LYS* 3.8 33.1 + - + -
117A LEU 3.2 9.2 + - - +
118A ARG 3.7 5.2 - - - +
119A GLN 3.2 0.6 - - - -
120A VAL* 1.3 77.1 - - - +
122A GLU* 1.3 64.0 + - + +
124A GLN* 4.0 12.8 + - - +
201A SO4 5.1 0.5 + - - -
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Residues in contact with GLU 122 (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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29A ILE* 4.0 17.1 - - + +
65A LYS* 5.6 0.2 - - - -
118A ARG 3.5 13.2 - - - +
119A GLN* 3.0 17.1 + - - +
121A ALA* 1.3 77.4 - - + +
123A ASN* 1.3 64.4 + - - +
124A GLN* 3.2 17.0 - - - +
201A SO4 2.5 40.3 + - - -
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Residues in contact with ASN 123 (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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61A ARG* 4.0 8.2 - - - +
116A TYR* 6.0 0.2 - - - -
119A GLN* 2.9 46.1 + - - +
120A VAL* 3.3 22.1 + - - +
122A GLU* 1.3 77.6 - - - +
124A GLN* 1.3 72.8 + - - +
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Residues in contact with GLN 124 (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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61A ARG* 3.4 34.8 + - - +
65A LYS* 5.6 5.2 - - - +
120A VAL 3.4 9.0 + - - -
121A ALA 4.0 8.5 + - - +
122A GLU 3.2 19.0 - - - +
123A ASN* 1.3 83.8 - - - +
201A SO4 4.8 11.4 + - - +
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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