Contacts of the strand formed by residues 79 - 87 (chain A) in PDB entry 1PSN
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 SER 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A SER* 5.4 1.7 + - - -
73A ILE 3.4 10.5 + - - -
74A THR* 4.5 12.2 + - - +
75A TYR* 5.2 1.8 - - - -
78A GLY* 1.3 75.4 - - - -
80A MET* 1.3 68.7 + - - +
81A THR* 5.3 3.8 - - - +
107A GLU* 3.7 5.9 - - - -
108A PRO* 3.2 37.7 + - - +
112A LEU* 3.8 10.3 - - - +
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Residues in contact with MET 80 (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 TRP* 3.8 50.0 - - + +
71A VAL* 4.5 9.4 - - + +
72A SER* 3.4 3.1 + - - -
73A ILE* 2.9 62.7 + - + +
75A TYR* 4.9 2.2 - - + -
79A SER* 1.3 77.9 + - - +
81A THR* 1.3 75.2 + - - +
82A GLY* 4.0 5.8 - - - +
102A GLY 5.0 0.2 - - - -
103A LEU 4.7 0.9 - - - -
104A SER* 3.6 34.8 - - - +
106A THR* 3.3 12.8 - - - +
107A GLU* 4.3 9.6 - - + -
108A PRO* 4.6 0.7 - - - -
112A LEU* 5.2 0.4 - - + -
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Residues in contact with THR 81 (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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70A THR* 6.4 0.7 - - - -
71A VAL 3.3 8.7 - - - -
72A SER* 3.4 24.2 - - - +
79A SER* 5.3 3.8 - - - +
80A MET* 1.3 76.9 - - - +
82A GLY* 1.3 52.1 + - - +
104A SER* 3.6 2.1 - - - -
105A GLU* 2.7 34.4 + - - +
106A THR* 2.8 39.0 + - - +
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Residues in contact with GLY 82 (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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70A THR* 3.2 10.4 - - - +
71A VAL* 2.8 36.5 + - - +
80A MET* 4.0 5.8 - - - +
81A THR* 1.3 75.9 - - - +
83A ILE* 1.3 61.9 - - - -
103A LEU 3.1 15.7 - - - -
104A SER* 4.0 2.2 - - - -
105A GLU* 3.7 10.9 + - - +
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Residues in contact with ILE 83 (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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44A TYR* 3.8 32.3 - - + -
64A TYR* 4.4 13.9 - - - +
66A SER* 6.2 2.5 - - - -
67A THR 5.2 8.5 - - - +
68A SER 6.3 0.9 - - - -
69A GLU 3.5 7.0 - - - +
70A THR* 3.9 15.3 - - + -
82A GLY* 1.3 76.5 - - - -
84A LEU* 1.3 65.7 + - - +
102A GLY* 3.4 1.9 - - - -
103A LEU* 2.8 51.3 + - + +
105A GLU* 3.8 22.9 - - + +
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Residues in contact with LEU 84 (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 ASN* 5.7 0.7 - - - +
64A TYR* 4.2 2.8 + - - -
67A THR* 2.8 40.2 + - - +
69A GLU* 2.8 24.4 + - + +
70A THR 3.8 17.5 - - - +
71A VAL* 3.8 24.7 - - + -
83A ILE* 1.3 74.9 - - - +
85A GLY* 1.3 58.0 + - - +
100A ILE* 4.2 28.3 - - + -
101A PHE 3.3 22.7 - - - +
102A GLY 3.9 0.7 - - - +
103A LEU* 4.5 0.9 - - - -
131A SER* 3.9 20.6 - - - +
133A ALA* 4.4 15.3 - - + -
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Residues in contact with GLY 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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64A TYR* 3.4 23.3 - - - -
65A GLN 3.5 6.7 - - - -
67A THR* 4.6 3.1 - - - -
83A ILE 3.7 2.2 + - - -
84A LEU* 1.3 74.1 - - - +
86A TYR* 1.3 63.9 + - - -
100A ILE* 3.3 5.4 - - - +
101A PHE* 2.9 39.1 + - - +
103A LEU* 3.8 3.5 - - - +
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Residues in contact with TYR 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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63A THR 3.7 2.2 - - - +
64A TYR* 3.5 3.5 - - - -
65A GLN* 2.9 58.1 + - + +
66A SER 5.4 0.2 - - - -
67A THR* 3.8 26.7 - - + -
85A GLY* 1.3 76.2 - - - -
87A ASP* 1.3 64.9 + - - +
98A ASN* 3.4 38.4 - - + +
99A GLN 3.3 3.8 - - - -
100A ILE* 3.7 36.2 - - + +
101A PHE* 4.0 0.4 - - - -
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Residues in contact with ASP 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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20A ILE* 4.1 7.0 - - + -
21A GLY* 3.3 14.5 - - - -
56A PHE* 3.5 14.4 - - - -
61A SER* 2.7 23.9 + - - -
63A THR* 2.7 37.9 + - - -
64A TYR* 3.7 5.7 + - + -
86A TYR* 1.3 72.1 - - - +
88A THR* 1.3 71.5 + - - +
89A VAL* 4.6 1.3 - - - -
98A ASN* 3.6 5.3 + - - +
99A GLN* 2.9 39.2 + - - +
101A PHE* 3.6 19.1 - - + -
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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