Contacts of the strand formed by residues 80 - 86 (chain A) in PDB entry 1LWT
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 GLU 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A THR 3.6 2.5 + - - +
79A HIS* 1.3 97.9 + - - +
81A LEU* 1.3 60.6 + - - +
82A VAL 3.5 1.0 + - - -
158A THR* 3.8 31.0 + - - +
159A ILE* 3.8 5.8 - - - -
160A GLU* 4.1 22.9 - - + +
453A HIS* 3.3 48.8 + - + +
454A ASN 4.8 3.0 + - - +
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Residues in contact with LEU 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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50A VAL* 4.7 2.0 - - + -
73A PHE* 3.6 24.5 - - + -
75A CYS* 4.9 3.6 - - - -
79A HIS* 4.3 10.5 - - + +
80A GLU* 1.3 72.9 - - - +
82A VAL* 1.3 60.1 + - - +
83A VAL* 2.9 23.7 + - + +
158A THR* 3.4 4.2 - - - -
159A ILE* 2.7 34.1 + - + +
161A ALA* 4.1 20.2 - - + +
164A LEU* 4.0 26.5 - - + -
177A GLN* 3.2 24.2 - - - +
421A PHE* 4.4 13.9 - - + -
423A LEU* 4.7 8.1 - - + -
452A VAL* 5.7 1.3 - - + -
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Residues in contact with VAL 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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30A LYS* 5.8 0.4 - - - +
80A GLU 3.5 1.2 + - - -
81A LEU* 1.3 70.2 - - - +
83A VAL* 1.3 64.0 + - - +
156A GLU* 5.3 11.2 - - + +
157A TRP 4.1 3.8 - - - +
158A THR* 4.2 7.6 - - + -
177A GLN* 3.7 25.5 + - - +
178A THR* 4.4 9.5 + - + +
443A GLN* 3.4 39.0 - - - +
451A VAL* 3.6 24.9 + - + +
452A VAL* 4.0 3.0 - - - +
453A HIS* 3.7 32.5 - - + +
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Residues in contact with VAL 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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81A LEU* 2.9 29.7 + - + +
82A VAL* 1.3 79.4 - - - +
84A ARG* 1.3 66.0 + - - +
156A GLU* 3.8 7.1 - - - +
157A TRP* 2.9 71.7 + - + +
158A THR 4.3 0.4 - - - +
159A ILE* 4.2 12.1 - - + -
164A LEU* 5.4 1.3 - - + -
175A THR* 4.1 12.3 - - + -
176A TYR 3.5 10.1 - - - +
177A GLN* 4.0 12.6 - - + +
178A THR* 5.8 1.1 - - - -
421A PHE* 4.6 7.0 - - + -
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Residues in contact with ARG 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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83A VAL* 1.3 78.7 - - - +
85A THR* 1.3 67.5 + - - +
154A TYR* 2.8 48.8 + - + -
155A PHE 3.2 15.9 - - - +
156A GLU* 3.9 25.5 + - + -
157A TRP* 3.7 1.8 - - - -
175A THR* 3.3 1.7 - - - +
176A TYR* 3.0 61.0 + - + +
178A THR* 3.7 30.3 + - + +
415A GLU* 5.7 5.9 + - - +
416A CYS* 3.8 33.9 + - - +
418A GLY 5.3 0.6 - - - +
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Residues in contact with THR 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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84A ARG* 1.3 73.0 + - - +
86A PRO* 1.3 86.0 - - + +
107A PHE* 3.9 17.5 - - + -
123A VAL* 4.3 15.0 - - + -
154A TYR* 3.7 3.8 - - - -
155A PHE* 2.5 44.1 + - + -
157A TRP* 2.7 36.9 - - - -
171A VAL* 4.6 3.1 - - + -
174A ALA 3.7 4.5 - - - +
175A THR* 3.0 15.1 + - - +
176A TYR* 4.8 0.4 - - - -
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Residues in contact with PRO 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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85A THR* 1.3 108.6 - - + +
87A ARG* 1.3 67.1 + - - +
88A SER* 5.3 4.9 - - - -
107A PHE* 3.5 11.4 - - + -
153A ALA 3.5 9.6 - - - +
154A TYR* 3.8 4.5 - - + -
155A PHE* 3.8 3.6 - - - -
174A ALA* 2.9 25.8 - - + +
176A TYR* 4.4 12.5 - - + +
420A TYR* 5.4 3.4 - - - +
26B G 4.2 15.9 - - - +
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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