Contacts of the strand formed by residues 77 - 88 (chain A) in PDB entry 4D85
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 LYS 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A TYR* 3.8 26.0 + - + +
71A VAL 3.5 7.4 - - - +
72A PRO* 3.8 20.0 - - + -
73A TYR* 4.5 5.8 - - - -
76A GLY* 1.3 82.1 - - - +
78A TRP* 1.3 65.7 + - - +
108A ASP* 3.1 44.5 + - + +
109A LYS* 4.7 15.9 - - + +
110A PHE* 3.5 8.5 - - - +
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Residues in contact with TRP 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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39A ASN* 4.0 12.3 - - + -
41A ALA* 3.3 20.0 - - + +
69A VAL* 4.1 22.9 - - + -
70A TYR* 3.3 10.0 - - - -
71A VAL* 3.1 59.3 + - + -
73A TYR* 2.8 43.3 + + - -
77A LYS* 1.3 74.8 - - - +
79A GLU* 1.3 70.8 + - - +
80A GLY 4.3 1.6 - - - -
102A ALA* 3.5 30.5 - - + -
104A ILE* 4.0 17.7 - - + -
106A GLU 3.6 11.7 - - - +
107A SER* 3.9 10.1 - - - +
110A PHE* 3.5 29.0 - + + -
120A ILE* 4.3 0.2 - - - +
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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
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69A VAL 3.3 15.9 - - - +
70A TYR* 4.1 16.5 - - + -
78A TRP* 1.3 82.1 - - - +
80A GLY* 1.3 65.2 + - - +
104A ILE* 3.8 2.4 - - - -
105A THR* 3.1 15.9 + - - +
106A GLU* 2.8 59.9 + - + +
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Residues in contact with GLY 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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68A GLY* 3.7 4.7 - - - -
69A VAL* 3.0 35.4 + - - -
78A TRP* 4.1 4.2 - - - -
79A GLU* 1.3 79.6 - - - +
81A GLU* 1.3 65.9 + - - +
103A ALA 2.9 16.8 - - - -
104A ILE* 4.2 0.7 - - - -
105A THR* 3.6 9.6 - - - -
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Residues in contact with GLU 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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56A ARG* 2.7 40.7 + - - +
62A TYR* 5.8 0.9 - - - +
64A ASP* 5.6 4.2 - - - +
67A LYS 4.1 4.9 - - - +
68A GLY* 4.9 1.6 - - - -
69A VAL* 4.5 0.4 - - - -
80A GLY* 1.3 77.7 - - - +
82A LEU* 1.3 65.9 + - - +
101A ILE 3.6 0.7 - - - +
103A ALA* 2.8 37.7 + - - +
105A THR* 3.6 22.8 + - + +
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Residues in contact with LEU 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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62A TYR* 4.4 3.4 + - - -
64A ASP* 3.7 8.0 - - - +
65A LEU* 2.9 34.8 + - + +
66A ARG 3.9 1.4 + - - -
67A LYS* 3.1 32.8 + - - +
68A GLY 3.7 20.2 - - - +
69A VAL* 3.4 26.7 - - + -
81A GLU* 1.3 75.3 - - - +
83A GLY* 1.3 59.1 + - - +
101A ILE 3.6 16.8 - - - +
102A ALA* 4.2 7.6 - - + +
131A PRO* 3.9 15.7 - - + -
135A LEU* 4.0 31.9 - - + -
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Residues in contact with GLY 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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62A TYR* 4.4 9.6 - - - -
63A ARG 3.1 13.5 - - - -
64A ASP* 4.2 1.1 - - - -
65A LEU* 3.3 14.3 - - - +
81A GLU 4.0 0.2 + - - -
82A LEU* 1.3 76.2 - - - +
84A THR* 1.3 70.2 + - - +
100A ASN* 3.4 1.0 - - - +
101A ILE* 2.9 30.4 + - - -
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Residues in contact with THR 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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62A TYR* 3.7 4.3 - - - -
63A ARG* 2.8 43.9 + - - +
65A LEU* 3.6 16.2 - - + +
83A GLY* 1.3 73.9 - - - +
85A ASP* 1.3 66.3 + - - +
98A ARG* 3.0 31.9 + - + +
99A ALA 3.3 13.5 - - - +
100A ASN* 3.1 28.5 - - - +
101A ILE* 4.4 3.1 - - - +
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Residues in contact with ASP 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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23A GLY* 3.3 14.7 - - - +
54A TYR* 2.6 28.1 + - - +
59A SER* 2.7 22.9 + - - -
61A THR* 2.7 24.8 + - - -
62A TYR* 3.7 8.0 - - - +
84A THR* 1.3 76.7 - - - +
86A LEU* 1.3 83.2 + - - +
87A VAL* 3.8 2.1 - - - +
97A VAL 3.3 0.5 - - - +
98A ARG* 3.2 29.1 - - - +
99A ALA 3.2 12.6 + - - +
101A ILE* 3.6 13.9 - - + +
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Residues in contact with LEU 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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21A THR 3.9 0.2 - - - +
22A VAL* 3.2 4.9 - - - -
23A GLY 2.8 31.5 + - - +
24A SER* 3.5 19.5 - - - +
61A THR* 3.5 23.6 - - + +
85A ASP* 1.3 84.5 + - - +
87A VAL* 1.3 61.1 + - - +
88A SER* 5.2 0.8 + - - -
96A THR* 3.7 20.6 - - + -
97A VAL 3.4 9.2 - - - +
98A ARG* 3.7 27.4 - - + +
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Residues in contact with VAL 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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20A MET* 3.8 19.1 - - + -
21A THR 3.4 9.0 - - - +
22A VAL* 3.9 10.1 - - + -
40A PHE* 3.9 23.8 - - + -
85A ASP 3.8 10.1 - - - +
86A LEU* 1.3 79.4 - - - +
88A SER* 1.3 71.0 + - - +
96A THR* 3.3 4.1 - - - -
97A VAL* 2.8 35.0 + - + +
99A ALA* 4.0 12.1 - - + -
101A ILE* 4.2 7.2 - - + -
138A PHE* 3.6 28.7 - - + -
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Residues in contact with SER 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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20A MET* 3.5 4.9 - - - +
21A THR* 2.6 50.3 + - - +
26A PRO* 5.6 0.5 - - - +
86A LEU 5.2 0.5 + - - -
87A VAL* 1.3 79.0 - - - +
89A ILE* 1.3 68.3 + - - +
90A PRO* 3.5 2.5 - - - +
95A VAL 3.5 19.7 - - - -
96A THR* 4.0 10.4 + - - +
138A PHE* 6.0 1.1 - - - -
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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
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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