Contacts of the helix formed by residues 40 - 57 (chain G) in PDB entry 7C17
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 THR 40 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ALA 4.2 4.3 + - - -
154F GLU* 3.0 35.2 + - - +
29G PRO* 5.9 0.4 - - - +
39G TYR* 1.3 75.5 - - - +
41G GLN* 1.3 64.1 + - + +
42G GLN* 3.2 24.0 - - + +
43G HIS* 3.0 30.5 + - + +
44G LEU* 3.0 25.7 + - - +
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Residues in contact with GLN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G TYR 4.0 1.2 + - - -
40G THR* 1.3 77.0 - - + +
42G GLN* 1.3 61.4 + - + +
44G LEU* 3.3 16.6 + - - +
45G ASN* 2.9 27.0 + - - +
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Residues in contact with GLN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G THR* 3.2 14.8 - - + +
41G GLN* 1.3 78.6 - - + +
43G HIS* 1.3 63.0 + - + +
45G ASN* 3.3 14.9 + - - +
46G GLU* 2.9 24.1 + - - +
70G PHE* 6.2 0.2 - - - -
71G ASN* 3.1 45.1 + - + +
75G ARG* 6.1 0.4 - - - +
124H GLU* 5.8 1.8 + - - -
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Residues in contact with HIS 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ALA 5.9 2.0 - - - -
26G VAL* 5.1 5.6 - - + -
27G THR* 2.7 42.1 + - - -
28G PRO 4.5 2.0 + - - -
29G PRO* 4.3 24.7 - - + +
39G TYR* 4.3 17.6 - + + -
40G THR* 3.0 38.2 + - + +
42G GLN* 1.3 78.7 - - + +
44G LEU* 1.3 57.6 + - - +
46G GLU* 3.4 10.6 + - - +
47G LEU* 2.9 28.2 + - - +
71G ASN* 5.9 0.2 - - - -
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Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G VAL* 5.6 8.1 - - + -
10G THR* 5.2 9.2 - - + +
39G TYR* 5.2 11.6 - - + +
40G THR 3.0 11.6 + - - +
41G GLN* 3.6 24.7 - - - +
42G GLN 3.3 0.2 - - - -
43G HIS* 1.3 75.4 - - - +
45G ASN* 1.3 58.3 + - - +
47G LEU* 3.2 7.8 + - - +
48G THR* 2.9 31.7 + - - +
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Residues in contact with ASN 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLN 2.9 16.7 + - - +
42G GLN* 3.3 19.8 + - - +
44G LEU* 1.3 74.1 - - - +
46G GLU* 1.3 60.0 + - - +
48G THR* 3.3 10.8 - - - +
49G LEU* 2.9 26.9 + - - +
70G PHE* 4.0 10.0 - - + -
71G ASN* 4.9 1.1 - - - +
124H GLU* 2.8 27.6 + - - -
127H SER* 3.1 23.0 + - - -
128H GLY 5.2 2.0 - - - +
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU 3.5 10.6 - - - +
26G VAL* 3.3 29.9 - - - +
27G THR* 4.5 9.5 + - + +
42G GLN 2.9 16.3 + - - +
43G HIS* 3.7 8.0 - - - +
44G LEU 3.3 0.2 - - - -
45G ASN* 1.3 75.7 - - - +
47G LEU* 1.3 61.3 + - - +
49G LEU* 3.4 1.4 + - - +
50G LEU* 2.9 34.2 + - - +
67G VAL* 3.3 42.1 - - + +
70G PHE* 3.8 13.6 - - + -
71G ASN* 3.6 20.4 - - - +
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G THR* 6.0 4.3 - - + +
12G LEU* 4.2 14.8 - - + +
17G ILE* 5.2 10.3 - - + -
39G TYR* 5.6 9.2 - - + -
43G HIS 2.9 17.9 + - - +
44G LEU* 3.2 10.3 + - - +
46G GLU* 1.3 81.5 + - - +
48G THR* 1.3 58.2 + - - +
50G LEU* 3.4 7.0 + - - +
51G ARG* 2.9 27.9 + - - +
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Residues in contact with THR 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 4.5 22.7 + - + +
12G LEU* 5.6 0.2 - - - -
44G LEU 2.9 16.6 + - - +
45G ASN* 3.3 24.9 - - - +
47G LEU* 1.3 75.0 - - - +
49G LEU* 1.3 60.3 + - - +
51G ARG* 3.7 8.2 - - - +
52G GLN* 2.9 32.1 + - - +
127H SER 4.2 8.4 + - - +
128H GLY 4.4 16.1 + - - +
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G ASN 2.9 18.1 + - - +
46G GLU* 3.7 4.7 - - - +
48G THR* 1.3 78.1 - - - +
50G LEU* 1.3 57.4 + - - +
52G GLN* 3.3 4.2 + - - +
53G ALA* 2.9 27.7 + - - +
67G VAL* 5.2 5.2 - - + -
70G PHE* 4.0 14.6 - - + -
123H ILE* 5.3 4.0 - - + +
126H LEU 5.0 1.4 - - - +
127H SER* 3.7 30.7 - - - +
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Residues in contact with LEU 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G TYR* 3.6 43.3 - - + +
25G LEU* 4.8 14.6 - - + +
26G VAL* 5.3 1.8 - - + -
46G GLU* 2.9 30.7 + - - +
47G LEU* 3.8 5.6 - - - +
49G LEU* 1.3 74.5 - - - +
51G ARG* 1.3 60.5 + - - +
53G ALA* 3.3 3.7 + - - +
54G ARG* 2.9 27.3 + - + +
60G LEU* 3.8 16.2 - - + -
63G SER* 3.3 36.3 - - - +
67G VAL* 4.1 12.5 - - + +
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Residues in contact with ARG 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 5.8 3.1 - - - +
12G LEU* 3.7 34.8 - - + -
20G TYR* 6.0 1.6 - - - -
47G LEU 2.9 17.6 + - - +
48G THR* 3.7 9.9 - - - +
49G LEU 3.3 0.2 - - - -
50G LEU* 1.3 77.7 - - - +
52G GLN* 1.3 57.9 + - - +
54G ARG* 3.8 4.3 - - - +
55G GLN* 2.9 41.0 + - - +
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Residues in contact with GLN 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G THR* 2.9 21.1 + - - +
49G LEU 3.3 4.7 + - - +
51G ARG* 1.3 75.8 - - - +
53G ALA* 1.3 61.0 + - - +
55G GLN* 4.3 14.7 + - - +
56G VAL* 3.3 39.0 + - + +
126H LEU* 3.8 24.2 - - + +
127H SER 4.5 7.7 + - - +
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LEU 2.9 16.1 + - - +
50G LEU* 3.7 7.4 - - - +
51G ARG 3.2 0.2 - - - -
52G GLN* 1.3 78.8 - - - +
54G ARG* 1.3 60.1 + - - +
56G VAL* 3.3 4.8 - - - +
58G PHE* 3.3 52.3 + - + +
63G SER* 3.9 20.4 - - - -
66G LEU* 4.5 8.3 - - + -
67G VAL* 6.3 0.4 - - + -
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Residues in contact with ARG 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541 G 3.5 17.6 + - - -
551 C 3.0 42.2 + - - +
20G TYR* 4.1 13.9 - - - +
50G LEU* 2.9 17.2 + - + +
51G ARG* 4.1 5.2 - - - +
53G ALA* 1.3 75.8 - - - +
55G GLN* 1.3 64.2 + - + +
56G VAL 3.5 0.2 + - - -
57G GLY* 3.6 11.9 + - - -
58G PHE 3.4 23.4 + - - -
59G ASN* 5.2 3.3 - - - +
60G LEU* 3.9 19.0 - - + +
63G SER* 5.3 1.1 - - - -
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Residues in contact with GLN 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G THR 5.9 1.6 + - - -
11G GLY 5.3 5.7 + - - -
12G LEU* 5.0 13.2 - - + +
51G ARG* 2.9 24.2 + - + +
52G GLN* 4.3 18.8 + - - +
53G ALA 3.4 0.2 - - - -
54G ARG* 1.3 78.6 - - + +
56G VAL* 1.3 62.8 + - + +
57G GLY* 3.4 0.4 - - - -
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Residues in contact with VAL 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLN* 3.3 31.6 + - + +
53G ALA 3.3 16.6 - - - +
55G GLN* 1.3 79.9 - - + +
57G GLY* 1.3 57.4 + - - +
58G PHE* 3.7 29.6 - - + -
97H GLU* 4.2 8.8 - - - +
98H LEU* 5.1 1.2 - - - +
101H MET* 3.3 27.1 - - + +
104H GLN* 3.4 26.2 - - - +
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Residues in contact with GLY 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G ARG* 3.6 12.4 + - - -
55G GLN 3.4 2.8 - - - -
56G VAL* 1.3 80.5 - - - +
58G PHE* 1.3 71.0 + - - +
59G ASN 3.9 0.9 + - - -
91G ILE* 4.3 14.7 - - - +
98H LEU* 4.8 9.7 - - - +
101H MET* 4.3 7.1 - - - +
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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
------------------------------------------------------------
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