Contacts of the strand formed by residues 99 - 106 (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 GLN 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.2 8.7 - - + +
86A TYR* 3.3 3.2 - - - -
87A ASP 2.9 34.2 + - - +
89A VAL* 3.7 19.1 - - + -
96A ASP* 2.6 38.5 - - - +
98A ASN* 1.3 74.4 - - - +
100A ILE* 1.3 89.9 + - - +
101A PHE* 3.4 5.9 - - - -
134A THR* 3.0 23.6 + - - -
135A PRO 4.0 4.8 + - - -
136A VAL* 3.5 12.5 - - - +
139A ASN* 3.1 25.9 + - - +
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Residues in contact with ILE 100 (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 LEU* 4.7 4.3 + - - +
67A THR* 4.9 3.4 - - + -
69A GLU* 6.4 0.2 - - + -
84A LEU* 4.2 32.8 - - + -
85A GLY 3.3 12.3 - - - +
86A TYR* 3.7 39.8 - - + +
98A ASN 3.6 4.9 + - - -
99A GLN* 1.3 96.7 + - - +
101A PHE* 1.3 65.7 + - - +
133A ALA* 3.9 14.3 - - + +
134A THR* 3.6 40.5 - - - +
139A ASN* 5.6 0.2 - - - -
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Residues in contact with PHE 101 (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* 3.6 28.3 - - + -
38A LEU* 3.4 32.5 - - + +
40A VAL* 3.9 24.7 - - + -
56A PHE* 3.8 21.3 - + - -
64A TYR* 4.4 1.6 - + - -
84A LEU* 3.3 11.2 - - - -
85A GLY 2.9 40.0 + - - +
86A TYR 4.0 2.5 - - - -
87A ASP* 3.6 28.5 - - + -
89A VAL* 4.8 4.3 - - + -
99A GLN 3.4 14.1 - - - +
100A ILE* 1.3 76.7 - - - +
102A GLY* 1.3 70.5 - - - +
103A LEU* 3.7 20.9 - - + -
133A ALA* 6.1 0.7 - - - -
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Residues in contact with GLY 102 (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 LEU 2.9 13.5 + - - -
39A TRP* 3.2 12.5 - - - +
40A VAL* 3.0 28.9 + - - +
71A VAL* 4.2 10.8 - - - -
80A MET* 5.0 1.1 - - - -
83A ILE 3.4 6.7 - - - -
84A LEU* 3.9 10.3 - - - +
101A PHE* 1.3 77.2 - - - +
103A LEU* 1.3 62.5 + - - -
104A SER 4.0 0.2 - - - -
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Residues in contact with LEU 103 (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 VAL* 3.7 3.8 - - - -
42A SER* 3.6 19.1 - - - +
44A TYR* 4.2 8.7 - - + -
56A PHE* 3.7 19.7 - - + -
58A PRO* 3.6 30.3 - - + -
64A TYR* 3.7 23.6 - - + +
82A GLY* 3.1 1.1 - - - -
83A ILE* 2.8 49.9 + - + +
85A GLY 3.8 11.7 - - - +
101A PHE* 3.7 24.7 - - + +
102A GLY* 1.3 71.7 - - - -
104A SER* 1.3 66.0 + - - +
105A GLU* 4.4 0.9 - - - +
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Residues in contact with SER 104 (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* 4.5 1.3 - - - -
40A VAL 3.0 13.3 + - - -
41A PRO* 3.1 12.5 - - - +
42A SER* 2.7 28.1 + - - +
44A TYR 4.0 0.2 - - - -
45A CYS* 3.5 15.6 + - - +
80A MET* 3.6 20.8 - - - +
81A THR 3.6 6.3 - - - -
102A GLY 4.0 1.0 - - - -
103A LEU* 1.3 70.5 - - - +
105A GLU* 1.3 61.3 + - - +
106A THR 4.5 0.2 - - - -
107A GLU* 2.8 38.1 + - - -
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Residues in contact with GLU 105 (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* 3.7 28.8 - - + +
45A CYS* 3.4 21.8 - - - -
46A SER 4.2 1.9 + - - -
47A SER* 4.1 1.9 + - - -
70A THR* 4.8 5.5 - - - +
81A THR* 2.7 20.0 + - - +
82A GLY* 4.3 12.3 + - - +
83A ILE* 3.8 25.3 - - + +
103A LEU 3.5 2.7 + - - +
104A SER* 1.3 76.9 - - - +
106A THR* 1.3 65.7 + - + +
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Residues in contact with THR 106 (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 CYS* 4.3 0.2 - - - -
47A SER* 3.5 9.2 - - - +
80A MET* 3.3 3.5 - - - +
81A THR* 2.8 53.3 + - - +
104A SER* 4.2 0.5 - - - -
105A GLU* 1.3 86.3 - - + +
107A GLU* 1.3 69.7 + - - +
108A PRO* 3.7 17.2 - - - +
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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