Contacts of the helix formed by residues 56 - 69 (chain A) in PDB entry 4GL5
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 ILE 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A CYS* 3.4 30.5 + - + +
54A MET 3.3 3.9 - - - +
55A GLY* 1.3 85.2 - - - +
57A GLY* 1.3 70.1 + - - +
59A LEU* 3.1 18.0 + - + +
60A ILE* 3.1 33.1 + - + +
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Residues in contact with GLY 57 (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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50A PRO* 6.0 0.2 - - - -
51A GLY 3.4 22.7 - - - -
53A CYS* 3.6 9.4 - - - +
56A ILE* 1.3 79.4 - - - +
58A PRO* 1.3 70.8 - - - +
59A LEU 2.9 1.7 + - - -
60A ILE* 3.0 27.1 + - - +
61A SER* 3.1 6.9 + - - -
88A TRP* 3.7 9.2 - - - -
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Residues in contact with PRO 58 (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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52A TYR* 3.5 34.1 - - + -
55A GLY* 4.8 5.4 - - - +
56A ILE 3.9 2.7 - - - +
57A GLY* 1.3 85.2 - - - +
59A LEU* 1.3 68.5 + - + +
61A SER* 3.5 1.6 + - - +
62A HIS* 3.3 26.0 + - - +
88A TRP* 3.5 48.1 - - + +
90A SER 4.6 7.2 - - - +
91A GLY* 5.3 3.8 - - - +
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Residues in contact with LEU 59 (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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55A GLY 3.5 20.0 - - - +
56A ILE* 3.1 17.6 + - + +
57A GLY 2.9 1.8 + - - -
58A PRO* 1.3 83.0 - - + +
60A ILE* 1.3 62.8 - - + +
62A HIS* 4.3 2.4 - - + +
63A GLY* 3.0 25.8 + - - -
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Residues in contact with ILE 60 (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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50A PRO* 4.9 15.7 - - + -
56A ILE* 3.1 26.8 + - + +
57A GLY* 3.0 25.3 + - - +
59A LEU* 1.3 76.5 - - + +
61A SER* 1.3 71.4 + - - +
63A GLY* 3.4 1.7 + - - -
64A ARG* 2.7 37.1 + - - +
77A TYR* 4.0 10.8 - - + +
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Residues in contact with SER 61 (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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50A PRO* 5.2 1.3 - - - -
57A GLY 3.1 14.9 + - - -
58A PRO 3.5 3.1 + - - -
60A ILE* 1.3 77.9 - - - +
62A HIS* 1.3 74.1 + - - +
64A ARG* 3.1 9.7 + - - +
65A PHE* 3.1 20.8 + - - -
77A TYR* 3.3 22.0 - - - -
87A VAL* 3.6 20.0 - - - -
88A TRP* 3.0 31.8 + - - -
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Residues in contact with HIS 62 (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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58A PRO 3.3 16.9 + - - +
59A LEU* 4.3 2.7 - - + +
61A SER* 1.3 80.2 + - - +
63A GLY* 1.3 65.6 + - - +
65A PHE* 2.8 18.5 + - + +
66A LEU* 3.1 23.6 + - + +
88A TRP 3.3 10.0 + - - +
89A ILE* 4.1 10.3 - - + +
90A SER* 3.0 39.2 + - - +
229A ILE* 2.9 30.0 + - + -
231A PRO* 3.5 36.2 - - + +
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Residues in contact with GLY 63 (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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59A LEU 3.0 20.2 + - - -
60A ILE 3.6 1.3 - - - -
62A HIS* 1.3 78.1 - - - +
64A ARG* 1.3 59.2 + - - +
66A LEU* 3.4 14.4 + - - +
67A TRP* 3.2 24.1 + - - +
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Residues in contact with ARG 64 (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 ILE* 2.7 21.6 + - - +
61A SER 3.2 10.3 - - - +
62A HIS 3.1 0.2 - - - -
63A GLY* 1.3 73.8 - - - +
65A PHE* 1.3 53.1 + - - +
67A TRP* 3.2 4.1 + - - +
68A MET* 2.6 73.7 + - + +
73A ALA* 4.6 2.0 - - + -
76A TYR* 3.1 48.8 + - - -
77A TYR* 3.2 33.7 + - + +
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Residues in contact with PHE 65 (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 SER 3.1 22.7 + - - -
62A HIS* 2.8 10.2 + - + +
64A ARG* 1.3 78.0 - - - +
66A LEU* 1.3 57.3 + - - +
69A GLY* 2.8 31.5 + - - -
70A ILE* 3.7 39.8 + - + +
73A ALA* 3.7 30.7 - - + -
74A CYS* 3.9 15.7 - - - -
77A TYR* 4.0 12.8 - + - -
87A VAL* 3.8 24.2 - - + -
89A ILE* 4.1 28.9 - - + -
96A ILE* 4.6 11.4 - - + -
229A ILE* 4.0 17.3 - - + -
395A ILE* 4.2 1.3 - - + -
476A ASP* 5.0 0.3 - - - +
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Residues in contact with LEU 66 (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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62A HIS* 3.1 34.8 + - + +
63A GLY* 3.8 15.3 - - - +
65A PHE* 1.3 77.1 - - + +
67A TRP* 1.3 62.4 + - - +
69A GLY* 4.6 1.6 + - - -
229A ILE* 3.9 19.7 - - + +
230A LYS* 3.8 38.1 - - + +
231A PRO* 3.9 20.4 - - + -
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Residues in contact with TRP 67 (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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63A GLY 3.2 16.2 + - - +
64A ARG* 3.9 2.9 - - - +
66A LEU* 1.3 78.9 - - - +
68A MET* 1.3 75.4 + - + +
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Residues in contact with MET 68 (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 ARG* 2.6 65.2 + - + +
67A TRP* 1.3 86.1 - - + +
69A GLY* 1.3 59.7 + - - +
72A SER* 3.2 23.3 + - - +
73A ALA* 4.0 20.0 - - + +
76A TYR* 4.1 20.2 - - + -
79A ARG* 6.0 0.2 - - - +
475A HIS* 4.5 2.6 + - - +
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Residues in contact with GLY 69 (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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65A PHE 2.8 17.6 + - - -
66A LEU 4.5 1.5 - - - -
67A TRP 3.6 0.8 - - - -
68A MET* 1.3 73.8 - - - +
70A ILE* 1.3 68.5 + - - -
71A GLY 2.8 5.5 + - - -
72A SER* 2.9 14.2 + - - -
73A ALA* 3.0 10.9 + - - +
475A HIS 3.4 8.1 - - - -
476A ASP* 3.3 16.4 - - - -
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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