Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 3FA6
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 THR 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LYS 3.8 0.9 - - - +
45A GLN* 3.6 2.4 - - - +
46A GLU* 2.8 48.2 + - + +
48A ASP* 1.3 78.2 - - - +
50A PHE* 1.3 68.3 + - - +
65A PHE 3.5 9.2 - - - +
66A LYS* 2.9 38.4 + - + +
70B GLU 5.4 6.1 - - - +
82B LYS* 6.2 1.6 - - - +
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Residues in contact with PHE 50 (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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3A PHE* 4.1 9.6 - + + -
43A ILE* 4.0 19.5 - - + -
44A LYS 3.5 1.8 - - - -
45A GLN* 3.4 38.4 - - + -
47A GLY 3.8 15.3 - - - -
48A ASP 3.7 5.4 - - - -
49A THR* 1.3 82.4 - - - +
51A TYR* 1.3 60.2 + - - +
52A ILE* 4.7 6.1 - - + -
63A ILE 3.8 0.6 - - - +
64A ASN* 3.4 6.1 - - - +
65A PHE* 2.8 70.7 + + + +
67A VAL* 4.0 9.4 - - + -
87A TRP* 3.8 16.6 - + - -
93A MET* 3.6 30.1 - - + -
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Residues in contact with TYR 51 (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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42A GLU* 4.4 15.0 - - - -
43A ILE* 3.4 4.0 - - - +
44A LYS* 2.9 52.6 + - + +
50A PHE* 1.3 73.2 - - - +
52A ILE* 1.3 66.9 + - - +
53A LYS* 3.5 34.5 + - + +
62A GLU* 2.6 39.1 + - + -
63A ILE 3.3 7.2 - - - -
64A ASN* 3.5 20.9 - - - +
72B GLU* 3.4 59.8 + - + +
73B GLU 4.8 0.2 + - - -
74B GLN* 4.6 2.4 - - - +
80B PRO* 6.0 0.9 - - - +
82B LYS* 5.9 1.3 - - - +
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Residues in contact with ILE 52 (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 VAL* 4.4 5.6 - - + -
42A GLU 3.3 9.0 - - - +
43A ILE* 4.3 18.4 - - + -
50A PHE* 4.7 5.2 - - + -
51A TYR* 1.3 83.4 - - - +
53A LYS* 1.3 62.5 + - - +
54A VAL* 4.0 22.4 - - + -
61A THR 3.6 1.4 - - - +
62A GLU* 3.3 3.1 - - - +
63A ILE* 2.8 43.2 + - + +
65A PHE* 3.8 30.5 - - + -
109A TRP* 4.4 7.2 - - + -
111A LEU* 3.7 28.3 - - + -
138A LSR 4.3 13.9 - - + -
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Residues in contact with LYS 53 (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 ALA 3.5 1.4 - - - +
41A VAL* 3.4 4.3 - - - +
42A GLU* 2.8 56.7 + - + +
51A TYR* 3.5 29.2 + - + +
52A ILE* 1.3 72.5 - - - +
54A VAL* 1.3 64.2 + - - +
55A SER* 3.8 18.1 + - - +
60A THR* 3.9 19.7 - - + -
61A THR 3.2 2.5 - - - -
62A GLU* 3.9 11.9 - - + +
74B GLN* 2.6 33.7 - - - +
80B PRO* 5.3 4.4 - - - +
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Residues in contact with VAL 54 (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* 4.0 20.4 - - + -
40A ALA 3.3 7.2 - - - +
41A VAL* 4.3 7.2 - - + -
52A ILE* 4.0 14.4 - - + -
53A LYS* 1.3 77.2 - - - +
55A SER* 1.3 64.1 + - - +
56A THR* 4.8 4.1 - - + +
59A ARG 3.8 1.6 - - - +
60A THR* 3.5 2.1 - - - -
61A THR* 2.8 42.2 + - + +
63A ILE* 5.6 0.4 - - + -
138A LSR 3.8 63.9 - - + -
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Residues in contact with SER 55 (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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38A LYS 4.4 1.0 - - - +
39A PRO* 3.5 3.3 - - - +
40A ALA* 2.8 48.7 + - - +
53A LYS* 3.8 25.1 + - - +
54A VAL* 1.3 74.8 + - - +
56A THR* 1.3 61.9 + - - +
59A ARG 3.5 4.0 - - - -
60A THR* 4.2 6.5 + - - +
59B ARG* 4.4 10.3 - - - -
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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