Contacts of the helix formed by residues 74 - 89 (chain A) in PDB entry 5D4P
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.6 31.4 - - + +
32A GLY 4.2 4.9 - - - +
33A VAL* 4.0 29.6 - - + +
70A VAL* 4.2 9.0 - - + -
71A PRO* 2.9 32.4 + - + +
73A GLU* 1.3 95.5 - - + +
75A VAL* 1.3 64.8 + - - +
76A GLY 3.4 1.3 - - - -
77A PRO* 3.1 9.9 - - + +
78A LEU* 3.0 28.9 + - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 3.8 35.9 - - + -
12A LEU* 4.4 10.5 - - + -
70A VAL* 4.1 12.6 - - + -
71A PRO 4.3 0.4 - - - +
72A GLU* 3.2 15.3 + - + +
74A LEU* 1.3 77.6 - - - +
76A GLY* 1.3 58.0 + - - +
78A LEU* 3.8 5.4 - - - +
79A LEU* 2.9 50.8 + - + +
95A VAL* 4.7 11.0 - - + -
6C LEU* 4.4 14.4 - - + -
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU 4.6 1.2 + - - -
73A GLU 4.6 0.8 + - - -
75A VAL* 1.3 80.4 - - - +
77A PRO* 1.3 62.7 - - - +
79A LEU* 3.2 6.8 + - - +
80A GLU* 2.9 33.9 + - - +
4C ILE* 4.8 9.8 - - - +
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Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.2 2.3 - - - +
31A ALA* 5.3 9.4 - - + -
73A GLU 3.4 15.7 - - - +
74A LEU* 3.1 20.4 - - + +
76A GLY* 1.3 91.1 - - - +
78A LEU* 1.3 63.0 + - + +
80A GLU* 3.4 12.2 + - + +
81A GLY* 3.0 18.5 + - - -
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Residues in contact with LEU 78 (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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12A LEU* 4.1 24.5 - - + -
27A LEU* 4.0 20.3 - - + +
28A LEU* 3.9 26.9 - - + -
31A ALA* 3.7 26.2 - - + -
33A VAL* 3.9 20.9 - - + -
70A VAL* 4.1 15.5 - - + -
74A LEU* 3.0 23.5 + - + +
75A VAL 3.8 4.5 - - - +
77A PRO* 1.3 77.6 - - - +
79A LEU* 1.3 58.8 + - - +
81A GLY* 3.0 4.0 + - - -
82A PHE* 2.9 37.6 + - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.3 6.1 - - + -
75A VAL* 2.9 37.3 + - + +
76A GLY* 3.8 4.0 - - - +
78A LEU* 1.3 75.3 - - + +
80A GLU* 1.3 58.1 + - - +
82A PHE* 3.6 6.4 - - + +
83A GLN* 2.8 32.1 + - - +
93A VAL* 4.0 32.1 - - + -
95A VAL* 4.6 6.5 - - + -
4C ILE* 4.6 18.2 - - + +
6C LEU* 3.6 33.4 - - + -
101C GLY* 5.9 1.6 - - - +
202C BCT 6.0 0.4 - - - +
203C BCT 4.6 21.7 + - - +
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Residues in contact with GLU 80 (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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76A GLY 2.9 15.8 + - - +
77A PRO* 3.6 13.9 - - - +
79A LEU* 1.3 76.5 - - - +
81A GLY* 1.3 63.9 + - - +
83A GLN* 3.4 8.5 + - - +
84A PRO* 3.1 21.1 - - - +
2C ASN* 3.5 38.7 + - + +
4C ILE* 5.1 10.1 - - + -
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Residues in contact with GLY 81 (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 PHE* 4.3 11.8 - - - -
27A LEU* 3.4 28.2 - - - +
77A PRO 3.0 11.0 + - - -
78A LEU 3.0 7.4 + - - -
80A GLU* 1.3 78.6 - - - +
82A PHE* 1.3 59.6 + - - +
84A PRO* 3.5 11.4 - - - +
85A PHE 4.5 0.5 + - - -
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Residues in contact with PHE 82 (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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12A LEU* 5.3 3.6 - - + -
14A ILE* 3.9 42.8 - - + -
16A LEU* 4.6 3.8 - - + -
23A PHE* 4.5 7.0 - + - -
24A ALA* 4.1 34.8 - - + -
27A LEU* 3.6 23.1 - - + -
28A LEU* 4.5 10.8 - - + -
78A LEU* 2.9 31.2 + - + +
79A LEU* 3.2 9.2 + - + +
81A GLY* 1.3 75.5 - - - +
83A GLN* 1.3 64.4 + - - +
84A PRO 3.5 0.2 - - - -
85A PHE* 3.2 13.0 + + - +
86A PHE* 3.0 51.8 + + + +
93A VAL* 4.8 7.6 - - + -
203C BCT 5.1 1.8 - - - -
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Residues in contact with GLN 83 (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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79A LEU 2.8 16.4 + - - +
80A GLU* 3.7 8.3 - - - +
82A PHE* 1.3 77.5 - - - +
84A PRO* 1.3 74.1 - - + +
86A PHE* 3.5 1.0 + - - -
87A GLU* 3.0 32.7 + - + +
203C BCT 3.9 28.5 + - - +
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Residues in contact with PRO 84 (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 GLU 3.1 16.4 - - - +
81A GLY* 3.5 12.3 - - - +
83A GLN* 1.3 97.5 - - + +
85A PHE* 1.3 61.3 + - - +
87A GLU* 3.3 28.6 - - - +
88A ALA* 3.4 10.2 + - - +
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Residues in contact with PHE 85 (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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16A LEU* 3.7 19.7 - - + -
20A HIS* 3.7 45.8 - + + -
23A PHE* 3.5 40.4 - + + -
81A GLY 4.5 0.4 + - - -
82A PHE* 3.2 15.2 + + - +
83A GLN 3.1 1.0 - - - -
84A PRO* 1.3 76.2 - - - +
86A PHE* 1.3 95.6 + + - +
87A GLU 3.0 4.0 - - - -
88A ALA 3.0 4.3 + - - -
89A HIS* 2.8 61.1 + + + +
90A SER 4.3 1.3 - - - -
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Residues in contact with PHE 86 (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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14A ILE* 3.9 19.1 - - + -
15A ILE 3.7 8.3 - - - -
16A LEU* 4.2 2.5 - - + -
82A PHE* 3.0 43.9 + + + +
83A GLN 4.4 1.3 - - - +
85A PHE* 1.3 91.1 - + - +
87A GLU* 1.3 61.8 + - - +
88A ALA 3.2 0.2 - - - -
89A HIS 3.2 15.2 - - - +
90A SER 3.5 17.7 - - - -
91A GLY* 3.4 33.9 - - - -
92A VAL 4.1 1.8 - - - -
93A VAL* 3.2 32.3 - - + -
102C ARG* 3.3 34.3 + - - +
203C BCT 4.8 8.3 - - - +
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Residues in contact with GLU 87 (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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83A GLN* 3.0 25.7 + - + +
84A PRO* 3.3 21.4 - - - +
86A PHE* 1.3 81.2 - - - +
88A ALA* 1.3 58.2 + - + +
102C ARG* 5.4 0.4 - - - +
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Residues in contact with ALA 88 (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 PRO 3.9 8.3 - - - +
85A PHE* 3.0 6.9 + - - +
87A GLU* 1.3 80.6 - - + +
89A HIS* 1.3 77.0 + - + +
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Residues in contact with HIS 89 (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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17A GLU* 4.5 7.0 - - - +
20A HIS* 3.5 29.3 + + - +
85A PHE* 2.8 57.2 + + + +
86A PHE* 3.2 22.5 - - - +
87A GLU 3.7 0.2 - - - -
88A ALA* 1.3 95.2 + - + +
90A SER* 1.3 65.2 + - - +
91A GLY 3.9 0.7 + - - +
201A ADP 4.9 0.2 + - - -
102C ARG* 5.3 0.3 + - - -
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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