Contacts of the strand formed by residues 58 - 66 (chain A) in PDB entry 1NFA
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 PRO 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASN 4.4 2.0 - - - +
57A GLU* 1.3 88.9 - - + +
59A LEU* 1.3 69.5 + - - +
60A MET* 5.6 0.5 - - - +
107A PRO* 5.4 8.7 - - + -
108A LEU 3.6 9.0 - - - +
109A LEU* 3.8 21.0 - - + -
110A PRO* 4.0 3.4 - - + -
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Residues in contact with LEU 59 (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 LEU* 5.8 6.7 - - + -
53A TYR* 3.8 34.8 - - + -
57A GLU* 3.3 38.4 - - + +
58A PRO* 1.3 84.1 - - - +
60A MET* 1.3 65.6 + - - +
61A LEU 3.8 0.4 + - - -
107A PRO* 3.2 3.7 - - - +
108A LEU* 2.9 32.5 + - - +
110A PRO* 4.3 11.0 - - + -
153A VAL* 4.6 12.8 - - + -
155A VAL* 4.1 15.5 - - + -
163A LEU* 4.1 17.9 - - + -
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Residues in contact with MET 60 (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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58A PRO 5.6 0.7 - - - +
59A LEU* 1.3 78.8 - - - +
61A LEU* 1.3 67.0 + - - +
62A GLN* 3.6 13.9 + - - +
105A GLU* 5.3 13.7 - - + -
106A ILE 4.8 2.2 - - - +
107A PRO* 4.0 28.0 - - + -
153A VAL* 3.9 10.9 - - - +
154A HIS 5.1 3.1 + - - +
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Residues in contact with LEU 61 (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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15A LEU* 5.0 13.0 - - + -
48A VAL* 4.3 11.9 - - + -
50A LEU* 5.7 6.3 - - + -
59A LEU 3.8 2.4 + - - -
60A MET* 1.3 73.7 - - - +
62A GLN* 1.3 63.5 + - - +
63A LEU* 3.0 42.1 + - + +
104A LEU 3.9 2.4 - - - +
105A GLU* 4.0 3.6 - - - +
106A ILE* 3.0 39.9 + - + +
108A LEU* 3.9 26.9 - - + +
151A PHE* 4.1 21.1 - - + -
152A ARG 4.9 3.1 - - - +
153A VAL* 4.0 16.8 - - + +
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Residues in contact with GLN 62 (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 MET* 3.6 16.2 + - - +
61A LEU* 1.3 76.4 - - - +
63A LEU* 1.3 57.6 + - - +
64A PHE* 4.2 1.8 + - - -
103A VAL* 6.0 5.8 - - + -
104A LEU 4.4 2.9 - - - +
105A GLU* 5.7 2.7 - - + +
150A VAL* 3.4 13.2 - - - +
151A PHE* 4.2 0.2 - - - -
152A ARG* 2.5 66.3 + - + +
154A HIS* 4.9 12.4 + - - +
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Residues in contact with LEU 63 (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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45A HIS* 5.7 0.2 - - + -
61A LEU* 3.0 23.1 - - + +
62A GLN* 1.3 73.7 - - - +
64A PHE* 1.3 69.8 + - - +
103A VAL* 4.8 0.6 - - - +
104A LEU* 2.7 61.5 + - + +
106A ILE* 4.0 12.1 - - + -
118A ILE* 2.9 38.4 - - + -
149A LEU* 2.9 31.9 - - + -
150A VAL 3.8 0.9 - - - +
151A PHE* 2.8 28.7 - - + -
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Residues in contact with PHE 64 (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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45A HIS* 6.2 0.2 - - - -
62A GLN 5.7 1.3 - - - -
63A LEU* 1.3 76.0 - - - +
65A ILE* 1.3 75.6 + - - +
66A GLY* 3.5 18.6 - - - -
73A LEU* 4.7 14.6 - - + -
74A ARG 4.1 10.5 - - - -
75A PRO* 4.5 12.1 - - + -
101A THR* 6.2 2.5 - - + -
102A LYS 4.0 10.3 - - - -
103A VAL* 2.9 41.1 - - + -
104A LEU* 3.8 13.7 - - - -
149A LEU* 4.0 5.7 - - - +
150A VAL* 3.4 53.2 + - + -
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Residues in contact with ILE 65 (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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45A HIS* 4.9 21.3 - - + +
64A PHE* 1.3 86.8 - - - +
66A GLY* 1.3 67.4 + - - +
76A HIS* 3.1 38.9 + - + +
79A TYR* 2.7 42.8 - - + +
80A GLN* 5.1 0.4 - - - -
102A LYS 5.4 3.3 + - - +
104A LEU* 4.8 3.3 - - + +
123A ILE* 5.8 2.7 - - + -
147A VAL* 4.0 16.8 - - + -
148A ARG 4.2 7.4 - - - +
149A LEU* 4.8 4.5 - - + +
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Residues in contact with GLY 66 (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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64A PHE* 3.5 15.9 + - - -
65A ILE* 1.3 79.8 - - - +
67A THR* 1.3 66.3 + - - -
73A LEU* 5.4 1.8 - - - -
74A ARG 2.9 17.7 - - - -
76A HIS 4.3 1.1 - - - -
148A ARG* 2.7 40.5 + - - +
150A VAL* 5.3 0.7 - - - -
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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