Contacts of the strand formed by residues 67 - 75 (chain A) in PDB entry 2FF3
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 ALA 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 3.7 4.0 - - - +
46A VAL* 3.0 28.1 + - + +
66A ASP* 1.3 75.1 - - - +
68A TYR* 1.3 66.7 + - - +
88A TRP 3.2 11.7 - - - +
89A LEU* 3.9 16.2 - - + -
93A CYS* 4.0 4.2 - - - +
97A GLU* 3.6 39.1 + - + +
98A SER 4.3 0.9 - - - +
101A ALA* 4.0 4.3 - - + -
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Residues in contact with TYR 68 (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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43A ILE* 4.1 4.3 - - + -
44A TRP 3.2 16.4 - - - +
45A ARG* 3.7 30.9 - - + +
46A VAL* 4.6 1.1 - - - +
54A VAL* 4.0 18.8 - - + -
61A ASP 4.2 3.9 + - - -
62A PHE* 3.3 36.4 - + + -
63A PHE* 3.1 57.5 + - - +
66A ASP* 4.0 8.3 - - + -
67A ALA* 1.3 75.7 - - - +
69A VAL* 1.3 61.2 + - - +
70A ILE* 3.8 18.4 - - + -
87A TYR* 3.3 7.1 - - - +
88A TRP* 2.8 42.7 + + + +
101A ALA* 4.3 2.9 - - - +
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Residues in contact with VAL 69 (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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43A ILE* 3.5 1.6 - - - -
44A TRP* 2.8 45.2 + - + +
46A VAL* 4.8 0.9 - - + -
51A LEU* 3.9 26.5 - - + -
68A TYR* 1.3 76.3 - - - +
70A ILE* 1.3 65.0 + - - +
85A LEU* 3.9 26.0 - - + -
86A HIS 3.5 5.2 - - - +
87A TYR* 4.7 0.7 - - + -
101A ALA* 3.7 31.2 - - - +
104A PHE* 4.2 5.6 - - + -
105A THR* 4.1 11.7 - - - +
108A LEU* 4.0 16.2 - - + -
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Residues in contact with ILE 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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41A LEU* 3.7 27.4 - - + -
42A GLN 3.4 5.8 - - - +
43A ILE* 3.9 22.7 - - + -
62A PHE* 4.2 3.1 - - + -
68A TYR* 3.8 22.7 - - + -
69A VAL* 1.3 81.1 - - - +
71A LEU* 1.3 63.1 + - - +
84A ASP 3.5 1.7 - - - +
85A LEU* 3.3 6.7 - - - +
86A HIS* 2.7 48.9 + - + +
88A TRP* 3.8 18.8 - - + -
130A PHE* 3.8 31.4 - - + -
133A TYR* 4.3 8.5 - - + -
134A PHE* 5.1 1.3 - - + -
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Residues in contact with LEU 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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35A ALA* 4.0 14.4 - - + -
36A GLY* 3.5 33.2 - - - +
40A GLY 3.9 1.2 - - - +
41A LEU* 3.6 6.3 - - - -
42A GLN* 2.9 45.2 + - + +
44A TRP* 3.8 17.4 - - + -
70A ILE* 1.3 73.3 - - - +
72A LYS* 1.3 60.7 + - - +
73A THR* 3.8 7.0 + - - +
83A TYR* 3.8 32.1 - - + -
84A ASP 3.5 11.2 - - - +
85A LEU* 3.9 22.0 - - + -
108A LEU* 5.5 0.7 - - + -
112A LEU* 4.4 10.5 - - + -
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Residues in contact with LYS 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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40A GLY* 3.6 21.1 - - - +
41A LEU* 3.8 19.0 - - + +
70A ILE* 4.1 1.4 - - - +
71A LEU* 1.3 71.8 - - - +
73A THR* 1.3 63.2 + - - +
74A VAL* 4.2 26.5 - - + +
82A GLN 3.4 4.9 - - - +
83A TYR* 3.6 1.4 - - - -
84A ASP* 3.0 36.0 + - + +
133A TYR* 3.6 52.7 - - + +
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Residues in contact with THR 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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36A GLY* 3.5 14.3 - - - +
38A GLU 3.4 31.2 - - - +
39A PRO* 3.2 4.7 - - + +
40A GLY* 2.8 37.9 + - - +
42A GLN* 4.6 2.1 + - - -
71A LEU* 3.8 7.5 + - - +
72A LYS* 1.3 76.4 - - - +
74A VAL* 1.3 64.9 + - - +
81A LEU* 3.8 19.7 - - + -
82A GLN 3.3 3.1 - - - -
83A TYR* 3.5 33.1 - - + -
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Residues in contact with VAL 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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39A PRO* 4.8 0.9 - - - -
72A LYS* 4.2 29.6 - - + +
73A THR* 1.3 78.1 - - - +
75A GLN* 1.3 76.2 + - - +
76A LEU* 3.3 2.4 + - + -
81A LEU* 3.5 6.9 - - - -
82A GLN* 2.9 66.5 + - + +
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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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39A PRO* 3.8 26.5 - - + +
74A VAL* 1.3 82.7 - - - +
76A LEU* 1.3 82.8 + - - +
77A ARG 4.0 0.7 + - - -
79A GLY* 3.1 28.3 + - - +
80A ASN 3.1 8.0 + - - -
81A LEU* 3.7 14.9 - - - +
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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