Contacts of the strand formed by residues 86 - 93 (chain A) in PDB entry 3LPJ
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 3.2 3.9 - - - -
81A VAL* 2.8 46.7 + - + +
84A PRO* 3.9 6.3 + - + +
85A PRO* 1.3 75.2 - - - +
87A THR* 1.3 64.0 + - - +
88A LEU* 3.7 6.7 + - + +
112A TYR 3.8 4.7 - - - +
113A TYR* 3.5 16.9 - - - -
114A GLN* 2.8 52.9 + - - +
117A LEU* 4.1 15.2 + - + +
118A SER* 4.2 14.8 - - - +
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Residues in contact with THR 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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78A GLU* 3.5 40.3 + - + +
79A MET 3.5 5.2 - - - +
80A THR* 3.9 12.1 - - + +
85A PRO* 4.0 3.5 + - - +
86A GLN* 1.3 72.5 - - - +
88A LEU* 1.3 72.6 + - - +
111A ARG* 3.3 33.0 + - - +
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Residues in contact with LEU 88 (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 GLU* 3.7 1.9 - - - +
79A MET* 2.9 35.5 + - + +
81A VAL* 4.0 23.1 - - + -
86A GLN* 3.7 9.2 + - + +
87A THR* 1.3 83.7 - - - +
89A ASN* 1.3 62.9 + - - +
90A ILE* 3.9 13.9 + - + +
101A VAL* 3.9 33.2 - - + -
102A GLY 5.0 0.4 - - - +
111A ARG* 3.8 20.0 - - + +
112A TYR* 4.1 21.1 - - - +
113A TYR* 4.1 10.8 - - + +
177A GLU* 3.5 19.3 - - + +
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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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68A ARG* 4.1 2.8 + - - -
76A TYR* 3.5 23.9 - - + -
77A VAL 3.7 1.6 - - - -
78A GLU* 3.8 23.2 - - - +
88A LEU* 1.3 71.9 - - - +
90A ILE* 1.3 66.2 + - - +
111A ARG* 3.2 14.6 + - - +
175A ASN* 3.2 38.8 + - - +
176A TRP* 3.5 2.6 - - - -
177A GLU* 2.8 35.9 + - - +
455A TLA 3.1 27.7 + - - +
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Residues in contact with ILE 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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76A TYR* 3.5 4.9 - - - +
77A VAL* 2.8 41.8 + - + +
79A MET* 3.6 32.8 - - + -
81A VAL* 6.1 0.7 - - + -
88A LEU* 3.9 17.5 - - + +
89A ASN* 1.3 84.7 - - - +
91A LEU* 1.3 64.1 + - - +
92A VAL 3.4 0.7 + - - -
99A PHE* 4.1 4.5 - - + -
101A VAL* 3.7 20.9 - - + -
178A GLY* 3.5 19.1 - - - +
179A ILE* 3.4 8.3 - - - +
180A LEU* 3.4 37.7 - - + +
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Residues in contact with LEU 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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74A GLY* 3.5 33.4 - - - -
75A TYR 3.5 14.1 - - - +
76A TYR* 3.9 4.5 - - - +
90A ILE* 1.3 70.8 - - - +
92A VAL* 1.3 68.9 + - - +
93A ASP* 3.4 5.2 + - + -
176A TRP* 3.9 25.1 - - + +
178A GLY 2.8 18.7 + - - +
179A ILE* 3.9 19.7 - - + +
180A LEU* 2.7 32.4 + - - +
290A SER 5.3 3.8 - - - +
291A GLY* 4.9 3.1 - - - -
456A Z75 3.6 38.4 - - + -
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Residues in contact with VAL 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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67A LEU* 4.0 20.9 - - + -
75A TYR* 2.9 24.8 + - + +
77A VAL* 3.9 27.6 - - + +
90A ILE 4.0 1.3 - - - +
91A LEU* 1.3 75.6 - - - +
93A ASP* 1.3 59.7 + - - +
180A LEU* 4.2 6.1 - - + -
182A LEU* 3.7 23.8 - - + -
213A LEU* 3.9 29.6 - - + -
215A LEU* 5.8 1.6 - - + -
235A MET* 4.1 7.9 - - - -
290A SER* 2.8 25.5 + - - +
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Residues in contact with ASP 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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91A LEU* 3.4 2.9 + - + +
92A VAL* 1.3 73.9 - - - +
94A THR* 1.3 59.0 + - - +
95A GLY* 2.8 20.1 + - - -
96A SER* 2.5 24.4 + - - +
179A ILE* 3.4 25.5 - - + +
180A LEU 3.0 15.6 + - - +
181A GLY* 3.4 2.3 - - - -
182A LEU* 2.9 25.0 + - - -
289A ASP* 3.0 14.9 - - - +
290A SER* 3.4 1.3 - - - -
291A GLY* 3.2 13.5 - - - +
456A Z75 2.6 21.0 + - - +
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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