Contacts of the strand formed by residues 88 - 96 (chain A) in PDB entry 1PMN
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 ARG 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.8 3.6 - - - -
83A ASP* 2.8 30.2 + - - +
86A LEU* 3.1 47.0 + - + +
87A ASP* 1.3 78.6 - - - +
89A ASN* 1.3 77.7 + - - +
90A VAL* 5.0 0.9 - - + -
127A LEU* 4.1 29.1 - - - +
147A GLU* 5.0 17.4 + - - +
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Residues in contact with ASN 89 (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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81A ALA 3.3 11.9 + - - +
82A TYR* 3.8 24.4 - - - +
88A ARG* 1.3 86.2 - - - +
90A VAL* 1.3 65.7 + - - +
148A LEU* 3.5 39.0 + - + +
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Residues in contact with VAL 90 (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* 4.0 25.1 - - + -
80A ALA* 3.6 3.3 - - - -
81A ALA* 2.8 44.1 + - - +
83A ASP* 3.9 22.2 - - + +
86A LEU* 5.0 2.5 - - + -
88A ARG* 4.1 3.8 - - - +
89A ASN* 1.3 82.5 - - - +
91A ALA* 1.3 60.5 + - - +
92A ILE* 4.3 8.3 - - + -
127A LEU* 3.8 26.2 - - + -
145A VAL* 3.9 13.0 - - + -
146A MET 3.3 9.2 - - - +
148A LEU* 3.6 11.2 - - - +
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Residues in contact with ALA 91 (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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78A VAL* 4.3 6.1 - - + -
79A CYS 3.2 9.6 - - - +
90A VAL* 1.3 74.2 - - - +
92A ILE* 1.3 58.0 + - - +
145A VAL* 3.4 4.9 - - - +
146A MET* 2.8 25.2 + - + +
148A LEU* 3.9 8.6 - - + +
501A 984 2.8 64.5 - - + +
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Residues in contact with ILE 92 (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 PHE* 3.9 22.1 - - + -
60A VAL* 4.5 8.1 - - + -
64A TYR* 3.8 35.9 - - + -
67A LEU* 4.6 11.4 - - + -
77A ILE 3.7 1.4 - - - +
78A VAL* 3.4 3.1 - - - -
79A CYS* 2.8 37.4 + - + +
81A ALA* 3.8 19.7 - - + -
90A VAL* 4.3 8.3 - - + -
91A ALA* 1.3 78.9 - - - +
93A LYS* 1.3 61.5 + - - +
130A PHE* 5.1 0.7 - - + -
143A TYR* 4.1 19.5 - - + -
144A LEU 3.2 9.2 - - - +
145A VAL* 4.2 16.2 - - + -
501A 984 3.8 1.1 - - - -
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Residues in contact with LYS 93 (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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75A GLN* 4.6 11.5 - - - +
76A GLY* 4.7 5.8 - - - +
77A ILE 3.3 8.1 - - - +
78A VAL* 3.9 16.6 - - + -
92A ILE* 1.3 77.0 - - - +
94A LYS* 1.3 63.8 + - - +
95A LEU* 3.7 27.4 - - + +
107A ARG* 4.3 19.8 - - - +
111A GLU* 5.0 4.0 + - - -
142A VAL 3.7 1.2 - - - +
143A TYR* 3.3 4.4 - - - -
144A LEU* 2.8 49.6 + - + +
501A 984 3.5 52.9 + - + +
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Residues in contact with LYS 94 (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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56A SER* 3.8 13.3 + - - +
57A THR* 2.9 26.8 + - - +
58A PHE* 3.5 31.1 - - + -
76A GLY* 3.3 23.2 - - - -
77A ILE* 3.0 15.1 + - + +
93A LYS* 1.3 72.5 - - - +
95A LEU* 1.3 70.0 + - - +
96A SER* 3.6 15.2 + - - -
141A ASP* 3.6 26.5 + - + -
142A VAL 3.7 2.7 - - - -
143A TYR* 3.4 32.9 + - + +
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Residues in contact with LEU 95 (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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75A GLN* 3.2 25.8 - - + +
93A LYS* 3.7 29.6 - - + +
94A LYS* 1.3 75.2 - - - +
96A SER* 1.3 59.8 + - - +
97A ARG 3.6 0.5 + - - -
98A PRO* 3.6 18.9 - - + +
108A ALA* 4.0 28.7 - - + +
112A LEU* 6.0 3.6 - - + -
141A ASP* 3.2 7.6 - - - +
142A VAL* 2.8 50.7 + - + +
144A LEU* 4.3 21.8 - - + -
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Residues in contact with SER 96 (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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75A GLN 4.8 2.6 + - - -
76A GLY* 5.5 0.6 - - - -
94A LYS* 3.6 20.4 + - - +
95A LEU* 1.3 69.6 - - - +
97A ARG* 1.3 77.4 + - - +
98A PRO* 3.1 1.9 - - - +
100A GLN* 3.3 14.2 + - - -
104A HIS* 5.3 1.0 + - - -
141A ASP* 3.4 13.5 + - - -
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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