Contacts of the strand formed by residues 84 - 92 (chain A) in PDB entry 2NDG
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 PHE 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A TRP* 4.0 3.4 - + - -
57A HIS 4.8 0.4 - - - -
58A LEU* 3.9 1.6 - - - -
59A HIS* 3.4 52.9 - + + +
62A PHE* 3.6 39.0 - + - -
82A ALA* 3.7 11.0 - - + -
83A GLY* 1.3 80.4 - - - +
85A ILE* 1.3 81.4 + - - +
86A LEU* 3.5 33.9 - - + -
107A LEU* 2.9 50.3 + - + +
217B ARG* 3.6 16.6 - - + +
218B KCR 4.7 5.6 - - + +
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Residues in contact with ILE 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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59A HIS* 5.5 1.4 + - - -
84A PHE* 1.3 81.4 - - - +
86A LEU* 1.3 63.2 + - - +
87A PRO* 3.4 11.7 - - + +
104A ASP* 3.8 40.4 - - + +
105A TYR 3.6 0.4 - - - -
106A ASP* 3.6 40.4 - - + +
217B ARG* 4.2 6.0 - - - +
223B LYS* 5.9 7.6 - - + +
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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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35A TRP* 3.6 5.6 - - + -
37A VAL* 4.8 0.4 - - + -
56A PHE* 3.6 28.5 - - + -
57A HIS 3.6 22.9 - - - +
58A LEU* 3.4 28.9 - - + -
84A PHE* 3.4 15.2 + - + -
85A ILE* 1.3 73.0 - - - +
87A PRO* 1.3 60.9 - - - +
88A ILE* 3.1 20.0 + - + +
105A TYR 2.8 31.1 + - - +
107A LEU* 3.3 46.0 - - + -
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Residues in contact with PRO 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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57A HIS* 3.2 61.5 + - + +
85A ILE* 3.4 13.2 - - + +
86A LEU* 1.3 80.6 - - - +
88A ILE* 1.3 60.8 + - - +
102A ARG* 4.1 18.4 - - + +
103A PHE 3.9 4.5 - - - +
104A ASP* 3.9 20.2 - - - +
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Residues in contact with ILE 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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16A LEU* 3.6 16.6 - - + -
37A VAL* 4.8 2.9 - - + -
38A PHE 4.9 1.3 - - - +
39A VAL* 3.3 27.6 - - + -
55A VAL 3.5 11.7 - - - +
56A PHE* 3.5 25.8 - - + +
86A LEU* 3.3 25.8 - - + +
87A PRO* 1.3 73.2 - - - +
89A GLU* 1.3 68.7 + - - +
90A VAL* 5.2 0.4 - - + -
101A VAL 3.6 0.2 - - - +
102A ARG* 3.1 4.7 - - - -
103A PHE* 2.6 40.6 + - + +
105A TYR* 3.4 38.8 - - + -
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Residues in contact with GLU 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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54A VAL* 3.4 7.5 - - - +
55A VAL* 2.8 50.5 + - + +
57A HIS* 2.7 33.6 + - + +
88A ILE* 1.3 78.0 - - - +
90A VAL* 1.3 62.2 + - - +
91A TYR* 3.8 10.6 + - + -
100A LYS* 2.7 42.2 + - + +
101A VAL 3.2 7.4 - - - +
102A ARG* 3.8 22.6 - - + +
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Residues in contact with VAL 90 (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 LEU* 3.8 21.3 - - + -
39A VAL* 4.1 26.2 - - + -
47A ILE* 4.1 4.7 - - + -
51A VAL* 3.2 43.1 - - + -
54A VAL* 3.5 10.5 - - + -
88A ILE* 5.2 0.2 - - + -
89A GLU* 1.3 77.6 - - - +
91A TYR* 1.3 62.4 + - - +
92A PHE* 3.7 2.5 + - + -
100A LYS* 3.3 2.4 - - - -
101A VAL* 2.9 41.5 + - + +
103A PHE* 4.1 14.4 - - + -
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Residues in contact with TYR 91 (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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51A VAL* 3.1 10.2 - - - +
52A GLU* 2.7 34.3 + - + -
53A LYS* 2.7 64.7 + - + +
54A VAL* 4.8 2.5 - - - -
55A VAL* 4.7 12.7 - - + +
66A LYS* 5.5 4.9 + - - -
89A GLU* 3.8 19.7 + - + -
90A VAL* 1.3 76.4 - - - +
92A PHE* 1.3 58.1 + - - +
99A ARG* 3.4 28.9 - - + -
100A LYS* 3.1 32.4 + - + -
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Residues in contact with PHE 92 (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 VAL* 5.2 0.4 - - + -
14A LEU* 3.5 18.6 - - + -
50A PHE* 3.4 14.8 - + - +
51A VAL* 3.7 21.8 - - + -
52A GLU* 4.2 8.3 - - - +
90A VAL* 4.2 2.2 - - + -
91A TYR* 1.3 79.3 - - - +
93A LYS* 1.3 62.1 + - - +
94A ASN* 3.6 22.3 + - - +
98A PRO 3.6 18.2 - - - -
99A ARG* 2.7 26.8 + - - +
100A LYS 4.1 8.1 - - - -
101A VAL* 3.2 40.2 - - + -
125A LEU* 3.2 25.8 - - + -
127A PHE* 4.4 16.4 - + - -
134A PHE* 5.0 4.7 - + + -
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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