Contacts of the strand formed by residues 74 - 86 (chain A) in PDB entry 4FRJ
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 GLY 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A PRO* 3.8 1.0 - - - +
71A TYR* 2.9 43.1 + - - +
72A THR 3.6 0.4 - - - -
73A GLN* 1.3 80.3 - - - +
75A LYS* 1.3 64.2 + - - +
106A ASP* 3.2 15.0 - - - -
107A LYS* 4.3 3.1 - - - -
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Residues in contact with LYS 75 (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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68A TYR* 3.5 30.0 + - + +
69A VAL 3.3 13.7 - - - +
70A PRO* 3.7 10.8 - - + -
71A TYR* 3.3 9.0 - - - -
74A GLY* 1.3 75.9 - - - +
76A TRP* 1.3 63.3 + - - +
77A GLU* 2.7 33.8 + - - -
104A GLU* 3.9 21.4 + - - -
105A SER* 3.3 7.1 - - - +
106A ASP* 2.8 48.7 + - + +
108A PHE* 3.8 2.9 - - - +
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Residues in contact with TRP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 4.0 21.1 - - + -
39A ALA* 3.6 17.2 - - + +
67A VAL* 3.6 22.9 - - + -
68A TYR* 5.0 0.7 - - - -
69A VAL* 2.8 70.7 + - + +
71A TYR* 4.5 0.2 - + - -
75A LYS* 1.3 78.8 - - - +
77A GLU* 1.3 83.2 + - - +
78A GLY* 4.1 3.8 - - - -
100A ALA* 3.5 33.2 - - + -
102A ILE* 3.8 20.2 - - + -
104A GLU 3.5 9.2 - - - +
105A SER* 4.1 8.3 - - - -
108A PHE* 3.8 33.4 - + + -
118A ILE* 5.0 4.0 - - + +
403A DWB 4.0 17.0 - + - -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL 3.5 15.9 - - - +
68A TYR* 3.6 25.9 - - + +
75A LYS* 2.7 30.5 + - - +
76A TRP* 1.3 81.3 - - - +
78A GLY* 1.3 58.8 + - - +
102A ILE* 3.5 5.4 - - - +
103A THR* 2.9 23.3 + - - +
104A GLU* 2.8 35.4 + - + +
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Residues in contact with GLY 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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66A GLY* 3.4 5.5 - - - -
67A VAL* 3.0 42.6 + - - +
76A TRP* 4.5 1.8 - - - -
77A GLU* 1.3 77.7 - - - +
79A GLU* 1.3 65.8 + - - +
101A ALA 3.1 14.4 - - - -
102A ILE* 4.2 0.2 - - - -
103A THR* 3.5 9.6 - - - -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 2.7 45.1 + - - +
62A ASP* 5.7 2.5 - - - +
65A LYS 3.8 6.5 - - - +
66A GLY* 4.5 2.5 - - - -
78A GLY* 1.3 77.2 - - - +
80A LEU* 1.3 65.4 + - - +
99A ILE 3.7 0.7 - - - +
100A ALA* 4.5 1.1 - - - -
101A ALA* 2.9 34.8 + - - +
103A THR* 3.7 23.7 + - + +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASN* 5.1 0.2 - - - +
60A TYR* 4.5 2.9 + - - -
62A ASP* 3.5 9.9 - - - +
63A LEU* 3.0 34.3 + - + +
64A ARG 4.0 1.7 + - - -
65A LYS* 2.9 44.7 + - + +
66A GLY 4.0 6.3 - - - +
67A VAL* 3.9 24.2 - - + -
79A GLU* 1.3 75.1 - - - +
81A GLY* 1.3 58.1 + - - +
98A ASN* 5.8 0.2 - - + -
99A ILE 3.6 4.3 - - - +
100A ALA* 3.9 16.6 - - + +
129A PRO* 3.9 19.1 - - + -
133A LEU* 3.7 34.1 - - + -
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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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60A TYR* 4.3 10.5 - - - -
61A ARG 3.0 14.8 - - - -
63A LEU* 3.7 11.0 - - - +
79A GLU 3.9 0.2 + - - -
80A LEU* 1.3 75.2 - - - +
82A THR* 1.3 68.8 + - - +
98A ASN* 3.5 2.8 - - - +
99A ILE* 2.9 32.8 + - - -
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Residues in contact with THR 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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52A TYR* 4.9 0.2 - - - -
60A TYR* 3.6 4.2 - - - -
61A ARG* 2.8 43.3 + - + +
63A LEU* 3.9 16.2 - - + -
81A GLY* 1.3 80.3 - - - +
83A ASP* 1.3 66.9 + - - +
96A ARG* 2.8 35.8 + - - -
97A ALA 3.3 12.1 - - - +
98A ASN* 3.5 19.5 - - - +
99A ILE* 4.5 2.2 - - - +
405A DMS 4.6 11.2 - - + +
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Residues in contact with ASP 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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21A GLY* 3.3 14.3 - - - +
52A TYR* 2.6 26.6 + - - +
57A SER* 2.9 23.8 + - - -
59A THR* 2.8 30.3 + - - -
60A TYR* 3.6 10.0 - - - +
82A THR* 1.3 77.2 - - - +
84A LEU* 1.3 72.1 + - - +
85A VAL* 3.7 3.5 - - - +
96A ARG* 3.4 9.7 - - - +
97A ALA 3.0 27.9 + - - +
99A ILE* 3.7 13.4 - - + +
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Residues in contact with LEU 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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19A THR 4.6 0.2 - - - -
20A VAL* 3.4 4.2 - - - -
21A GLY 2.8 29.0 + - - +
22A SER* 4.1 9.4 - - - +
59A THR* 4.0 31.6 - - + +
83A ASP* 1.3 79.8 + - - +
85A VAL* 1.3 60.6 + - - +
94A THR* 3.8 21.5 - - + -
95A VAL* 3.3 4.9 - - - +
96A ARG* 3.8 40.8 - - + +
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Residues in contact with VAL 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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18A MET* 3.5 31.6 - - + -
19A THR 3.3 11.2 - - - +
20A VAL* 4.3 2.9 - - + -
38A PHE* 4.0 20.0 - - + -
83A ASP 3.7 11.9 - - - +
84A LEU* 1.3 81.1 - - - +
86A SER* 1.3 64.5 + - - +
93A VAL 4.2 0.2 - - - +
94A THR* 3.4 6.2 - - - +
95A VAL* 2.8 36.5 + - - +
97A ALA* 3.8 17.0 - - + -
99A ILE* 4.0 11.0 - - + -
136A PHE* 3.7 18.0 - - + -
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Residues in contact with SER 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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18A MET* 3.4 6.6 - - - +
19A THR* 2.6 53.3 + - - +
85A VAL* 1.3 76.7 - - - +
87A ILE* 1.3 68.1 + - - +
88A PRO* 3.9 3.3 - - - +
91A PRO 5.8 0.2 - - - -
93A VAL 3.4 20.4 - - - -
94A THR* 3.9 11.7 - - - -
136A PHE* 6.0 0.2 - - - -
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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