Contacts of the strand formed by residues 68 - 77 (chain A) in PDB entry 4AG2
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 GLN 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A VAL 3.6 0.3 - - - +
55A LEU* 2.8 42.7 + - + +
66A THR 4.1 5.7 + - - +
67A TRP* 1.3 79.4 - - - +
69A LYS* 1.3 61.0 + - - +
70A LEU* 3.5 16.6 - - + +
99A ALA* 3.4 10.7 - - - +
100A SER* 2.8 59.3 + - - -
102A THR* 3.9 10.7 + - - +
105A VAL* 3.4 20.5 - - + +
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 5.2 6.7 + - - -
52A THR* 3.6 26.4 - - + +
53A VAL 3.3 4.0 - - - +
54A THR* 3.7 20.3 + - + +
63A GLU* 6.0 0.6 + - - -
67A TRP* 4.2 31.0 - - + -
68A GLN* 1.3 74.3 - - - +
70A LEU* 1.3 64.1 + - - +
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Residues in contact with LEU 70 (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 THR* 3.7 3.6 - - - +
53A VAL* 2.9 37.0 + - + +
55A LEU* 3.8 20.6 - - + -
68A GLN* 3.5 32.1 - - + +
69A LYS* 1.3 77.2 - - - +
71A GLU* 1.3 68.6 + - - +
95A LEU* 3.9 22.7 - - + -
96A LYS* 5.2 1.3 - - + +
97A GLU* 3.2 39.5 - - + +
98A LYS 4.0 4.0 - - - +
99A ALA* 4.0 13.7 - - - +
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Residues in contact with GLU 71 (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 SER* 5.0 6.8 - - - -
51A ILE 3.4 16.7 + - - +
52A THR* 2.8 28.7 + - - +
70A LEU* 1.3 74.0 - - - +
72A VAL* 1.3 65.4 + - - +
73A ILE* 5.5 1.1 - - + -
95A LEU* 3.5 3.9 - - - -
96A LYS* 2.9 46.9 + - + +
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Residues in contact with VAL 72 (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 SER* 6.0 1.4 - - - -
51A ILE* 3.0 48.1 + - + +
53A VAL* 3.8 19.7 - - + -
71A GLU* 1.3 78.2 - - - +
73A ILE* 1.3 63.6 + - - +
74A LYS 3.6 24.0 - - - +
75A GLN* 4.1 18.4 - - + +
93A LEU* 4.0 13.2 - - + -
94A LYS 3.5 10.5 - - - +
95A LEU* 4.0 9.0 - - + +
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Residues in contact with ILE 73 (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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71A GLU* 3.7 1.9 + - + -
72A VAL* 1.3 76.7 - - - +
74A LYS* 1.3 61.6 + - + +
94A LYS* 2.7 43.8 + - + +
95A LEU 3.9 14.1 - - - +
96A LYS* 3.6 44.6 - - + +
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Residues in contact with LYS 74 (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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72A VAL* 3.6 5.2 - - - +
73A ILE* 1.3 86.2 - - + +
75A GLN* 1.3 66.5 + - - +
76A PHE* 3.4 44.3 - - + -
92A LEU 3.9 0.5 - - - +
93A LEU* 3.6 2.6 - - - -
94A LYS* 2.7 40.4 + - + +
226A ASN* 4.9 3.8 - - - +
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Residues in contact with GLN 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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47A ALA* 3.5 15.1 - - - +
48A GLY 2.9 40.4 + - - +
49A ARG 3.9 11.5 + - - -
50A SER* 4.5 2.0 - - - +
51A ILE* 3.6 18.9 - - + +
72A VAL* 4.1 6.9 - - + +
74A LYS* 1.3 80.9 + - - +
76A PHE* 1.3 64.2 + - - +
77A ARG* 3.7 3.5 + - + +
91A MET* 4.0 8.7 - - - -
92A LEU 3.7 4.5 - - - -
93A LEU* 3.6 19.7 - - + -
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Residues in contact with PHE 76 (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 PHE* 3.8 23.3 - + - -
74A LYS* 3.4 55.9 - - + -
75A GLN* 1.3 71.9 - - - +
77A ARG* 1.3 65.9 + - - +
91A MET* 3.3 4.8 - - - -
92A LEU* 2.8 46.5 + - + +
94A LYS* 4.0 5.2 - - + -
218A TRP* 3.3 7.5 - - + -
222A ILE* 3.8 35.4 - - + -
226A ASN* 3.4 33.9 - - - -
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Residues in contact with ARG 77 (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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44A ALA* 3.4 41.7 + - + -
47A ALA* 4.1 15.4 - - + +
75A GLN* 3.7 5.5 + - + -
76A PHE* 1.3 77.0 - - - +
78A HIS* 1.3 71.8 + - - +
79A PRO* 3.2 7.4 - - - +
81A TYR* 3.9 20.7 + - + +
91A MET* 3.8 14.3 - - - +
218A TRP* 4.2 2.0 - - - -
31C ASP* 2.9 26.5 + - - -
34C SER* 2.7 28.9 + - - -
50C TYR* 5.6 0.4 + - - -
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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