Contacts of the strand formed by residues 161 - 168 (chain A) in PDB entry 1LKF
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 ASN 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ILE 3.4 4.9 + - - +
87A SER* 2.5 37.2 + - - -
88A SER 5.3 0.3 - - - +
96A VAL* 3.7 5.0 - - - +
156A ASN* 3.8 19.9 + - - +
157A THR* 3.3 6.7 - - - +
158A ASN* 2.8 55.4 + - - +
159A TYR 3.7 0.2 - - - -
160A LYS* 1.3 88.4 - - - +
162A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.5 1.8 - - - -
86A ILE* 2.8 44.8 + - + +
96A VAL* 3.9 10.8 - - + -
99A TYR* 3.5 44.2 - - + -
153A LEU* 3.9 9.0 - - + -
154A SER* 4.3 0.9 - - - -
156A ASN* 5.6 1.3 - - - -
157A THR* 3.8 5.6 - - - +
161A ASN* 1.3 77.3 - - - +
163A GLY* 1.3 62.0 + - - +
164A TRP* 3.8 27.1 - - + -
227A SER* 3.8 21.1 - - - -
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Residues in contact with GLY 163 (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 VAL 3.2 11.7 - - - -
85A SER* 4.1 6.5 - - - -
153A LEU* 3.2 15.9 - - - +
154A SER* 2.9 41.2 + - - -
156A ASN* 5.5 0.2 - - - -
157A THR* 3.4 1.0 + - - -
162A VAL* 1.3 78.8 - - - +
164A TRP* 1.3 64.4 + - - -
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Residues in contact with TRP 164 (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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82A TYR 3.7 0.6 - - - +
83A ASN* 3.3 6.7 - - - +
84A VAL* 3.0 46.1 + - + +
86A ILE* 3.9 24.2 - - + -
99A TYR* 3.8 12.6 - - + -
100A ALA 3.7 7.4 - - - -
101A PRO* 2.9 44.3 + - + -
151A THR* 4.1 7.0 - - + -
152A THR 3.3 7.0 - - - +
153A LEU* 3.6 22.8 - - + +
154A SER* 4.3 4.7 - - - +
162A VAL* 3.8 22.4 - - + -
163A GLY* 1.3 73.0 - - - -
165A GLY* 1.3 58.7 + - - +
166A VAL* 4.3 1.1 - - - -
225A PHE* 3.4 50.3 - + + -
226A LEU 3.5 27.8 - - - -
227A SER* 4.4 0.2 - - - -
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Residues in contact with GLY 165 (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 LYS* 3.9 11.2 - - - -
82A TYR 3.2 6.3 - - - -
83A ASN* 3.4 12.6 - - - -
150A ARG 3.2 1.4 - - - +
151A THR* 3.1 5.0 - - - -
152A THR* 2.8 38.5 + - - -
154A SER* 4.9 1.4 - - - +
164A TRP* 1.3 76.7 - - - +
166A VAL* 1.3 63.1 + - - +
167A GLU* 3.8 1.6 - - - -
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Residues in contact with VAL 166 (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 LYS* 3.2 2.8 - - - +
82A TYR* 2.8 45.0 + - + +
144A TYR* 4.7 0.2 - - + -
146A GLN* 3.5 26.2 - - + +
149A TYR* 3.6 9.0 - - + -
150A ARG 3.2 3.6 - - - -
151A THR* 3.8 13.0 - - - +
164A TRP 5.2 0.2 - - - -
165A GLY* 1.3 75.2 - - - -
167A GLU* 1.3 58.8 + - - +
216A LEU* 3.7 27.8 - - + -
221A PHE* 3.6 30.7 - - + -
225A PHE* 4.0 15.3 - - + -
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Residues in contact with GLU 167 (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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80A ALA 3.5 5.6 - - - +
81A LYS* 3.5 30.7 + - + -
149A TYR* 3.3 5.8 - - - -
150A ARG* 2.8 41.5 + - + +
152A THR* 5.3 5.0 + - - +
165A GLY 5.0 0.9 - - - -
166A VAL* 1.3 75.0 - - - +
168A ALA* 1.3 78.0 + - - +
169A HIS* 3.7 1.7 - - - +
181A ARG* 2.8 40.9 + - - +
267A LYS* 4.0 12.5 + - - -
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Residues in contact with ALA 168 (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 TRP* 3.5 38.8 - - + -
80A ALA 2.8 15.0 + - - +
149A TYR* 3.3 17.0 - - + -
167A GLU* 1.3 81.4 - - - +
169A HIS* 1.3 59.5 + - - +
171A ILE* 3.8 11.4 - - + -
180A GLY* 5.0 1.9 - - - -
181A ARG* 3.9 17.7 + - + +
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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