Contacts of the strand formed by residues 67 - 79 (chain A) in PDB entry 4PSQ
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 TRP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.0 35.6 + - + +
64A LEU* 3.0 64.7 + - + +
65A ASN 3.6 0.2 - - - -
66A ASN* 1.3 81.3 - - - +
68A ASP* 1.3 76.9 + - - +
69A VAL* 4.2 8.5 - - + -
208A EDO 3.6 26.2 - - - -
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Residues in contact with ASP 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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60A ARG* 2.7 44.6 + - + +
61A VAL 3.6 4.3 - - - +
62A ARG* 3.4 18.5 - - - +
63A LEU* 4.6 0.9 - - - +
64A LEU 3.7 8.7 - - - +
65A ASN 4.5 5.2 - - - +
66A ASN* 4.2 1.3 - - - -
67A TRP* 1.3 89.9 + - - +
69A VAL* 1.3 65.0 + - - +
173A TYR* 4.5 17.4 + - + +
208A EDO 3.2 16.1 + - - -
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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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60A ARG* 3.6 3.8 - - - -
61A VAL* 3.1 51.6 + - + +
63A LEU* 3.9 26.7 - - + -
67A TRP* 4.2 9.2 - - + -
68A ASP* 1.3 80.7 - - - +
70A CYS* 1.3 60.8 + - - +
71A ALA* 3.3 7.8 + - + +
173A TYR* 6.2 0.7 - - - -
208A EDO 3.6 29.2 - - - +
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Residues in contact with CYS 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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58A LYS* 5.5 1.3 - - - -
59A GLY 3.5 6.3 - - - +
60A ARG* 5.2 0.2 - - - -
69A VAL* 1.3 71.7 - - - +
71A ALA* 1.3 63.7 + - - +
72A ASP* 3.3 14.9 + - - +
173A TYR* 3.7 15.9 - - - -
174A CYS* 2.0 56.3 - - + -
208A EDO 3.5 20.0 + - - +
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Residues in contact with ALA 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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37A LEU* 4.4 15.3 - - + +
57A ALA 3.5 6.4 - - - +
58A LYS* 3.5 0.3 - - - -
59A GLY 2.8 34.4 + - - +
61A VAL* 3.9 21.5 - - + -
69A VAL* 3.3 5.7 + - + -
70A CYS* 1.3 69.9 - - - +
72A ASP* 1.3 61.6 + - - +
73A MET* 3.7 9.8 + - + +
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Residues in contact with ASP 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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57A ALA 3.8 3.1 - - - -
58A LYS* 3.7 35.7 - - + +
70A CYS* 3.3 17.3 + - - +
71A ALA* 1.3 73.5 - - - +
73A MET* 1.3 60.9 + - - +
92A GLY* 3.6 4.0 - - - -
93A VAL* 3.1 46.9 + - + +
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Residues in contact with MET 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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37A LEU* 3.7 28.3 - - + -
56A THR* 3.3 6.4 - - - -
57A ALA* 2.8 38.8 + - + +
71A ALA* 4.2 12.6 - - + +
72A ASP* 1.3 78.8 - - - +
74A VAL* 1.3 65.5 + - - +
90A TYR* 3.7 31.4 - - + -
91A TRP 3.3 12.3 - - - +
92A GLY* 4.2 5.4 - - - +
201A 2WL 3.8 58.8 - - + -
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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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54A SER* 6.1 0.9 - - - -
55A ALA 3.5 9.0 - - - +
56A THR* 4.6 12.8 - - + -
73A MET* 1.3 80.1 - - - +
75A GLY* 1.3 68.2 + - - +
76A THR* 5.0 2.7 - - + -
90A TYR* 3.2 4.5 - - - +
91A TRP* 2.9 69.2 + - + +
93A VAL* 3.5 27.6 - - + -
201A 2WL 3.8 4.4 - - - -
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Residues in contact with GLY 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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54A SER* 3.4 5.9 - - - -
55A ALA 2.7 39.9 + - - +
74A VAL* 1.3 77.6 - - - +
76A THR* 1.3 64.0 + - - +
77A PHE* 4.7 4.3 - - - -
88A MET* 4.4 4.9 - - - -
89A LYS 3.3 9.6 - - - -
90A TYR* 4.2 2.5 - - - -
91A TRP* 4.7 0.2 - - - -
201A 2WL 3.8 13.6 - - - -
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Residues in contact with THR 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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52A GLN* 3.6 19.3 - - - +
53A MET 4.1 4.5 - - - -
54A SER* 4.3 8.1 - - - +
74A VAL* 5.0 3.8 - - + -
75A GLY* 1.3 79.5 - - - +
77A PHE* 1.3 63.4 + - - +
78A THR* 5.0 1.0 + - - -
87A LYS 3.5 1.9 - - - +
88A MET* 3.6 1.5 - - - +
89A LYS* 2.9 50.9 + - - +
91A TRP* 3.7 23.8 - - + -
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Residues in contact with PHE 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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45A PHE* 3.8 23.6 - + - -
52A GLN* 3.5 25.1 + - - +
53A MET* 3.1 41.9 + - + +
54A SER* 3.7 7.0 - - - -
55A ALA* 3.7 27.4 - - + -
75A GLY 4.5 3.1 - - - -
76A THR* 1.3 73.6 - - - +
78A THR* 1.3 62.8 + - - +
79A ASP* 4.3 3.4 + - - +
86A PHE* 3.9 31.0 - - + -
87A LYS 3.4 1.8 - - - -
88A MET* 3.4 37.9 - - + -
104A HIS* 3.4 30.3 - + - -
201A 2WL 4.9 0.4 - + - -
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Residues in contact with THR 78 (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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76A THR 5.0 1.2 + - - -
77A PHE* 1.3 76.0 + - - +
79A ASP* 1.3 73.2 + - - +
80A THR* 4.2 2.0 - - + +
86A PHE* 3.4 6.8 - - - -
87A LYS* 2.9 45.3 + - + +
89A LYS* 6.2 0.5 - - - +
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Residues in contact with ASP 79 (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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17A LYS* 2.7 37.2 + - - +
52A GLN* 5.5 2.9 - - - +
53A MET 5.3 2.8 + - - -
77A PHE* 4.6 3.5 - - - +
78A THR* 1.3 85.3 - - - +
80A THR* 1.3 66.9 + - - +
83A PRO* 6.4 1.1 - - + -
86A PHE* 3.3 23.3 - - + -
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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