Contacts of the strand formed by residues 141 - 148 (chain K) in PDB entry 5KZ5
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 GLY 141 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123K TYR* 4.4 1.6 + - - -
136K LEU* 3.5 21.7 + - - +
139K ASP* 3.4 4.6 + - - +
140K LEU* 1.4 83.3 - - - +
142K THR* 1.4 68.3 + - - +
143K TYR* 4.9 0.7 - - - -
159K PRO* 4.4 14.6 - - - -
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Residues in contact with THR 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K TYR* 5.0 3.1 - - + -
133K THR* 4.7 10.9 - - + +
134K VAL 3.5 14.8 - - - +
135K LYS* 4.2 21.8 - - + -
141K GLY* 1.4 76.9 - - - +
143K TYR* 1.4 64.2 + - - +
144K VAL* 4.4 8.6 + - - +
157K SER 4.4 0.9 - - - +
159K PRO* 3.5 22.4 - - - +
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Residues in contact with TYR 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K THR* 3.9 2.1 - - - +
134K VAL* 3.2 39.9 + - + +
136K LEU* 3.4 38.9 - - + +
140K LEU 4.5 7.8 + - - -
142K THR* 1.4 74.7 - - - +
144K VAL* 1.4 61.8 + - - +
145K ILE* 3.7 4.2 - - + +
156K LEU* 4.1 7.6 - - + -
157K SER 3.4 7.4 - - - +
158K SER* 3.4 24.5 - - - -
159K PRO* 3.5 24.3 - - + +
160K SER* 4.8 6.2 - - - -
186K LEU* 3.5 26.9 - - + -
189K GLU* 3.4 42.7 + - + +
190K LEU* 5.1 2.2 - - + -
193K ALA* 5.6 1.7 - - - +
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Residues in contact with VAL 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K VAL* 3.4 28.5 - - + -
132K LEU 4.3 2.0 - - - -
133K THR* 4.5 16.8 - - + +
142K THR* 4.9 8.7 - - - +
143K TYR* 1.4 74.2 - - - +
145K ILE* 1.4 60.6 + - - +
146K ASN* 3.6 13.7 - - + +
155K TRP 3.6 2.4 - - - +
156K LEU* 3.9 0.5 - - - -
157K SER* 2.9 46.8 + - - +
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Residues in contact with ILE 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K LEU* 3.6 8.3 - - + +
106K LEU* 3.9 21.3 - - + -
110K PHE* 4.6 3.1 - - + -
131K VAL* 3.6 0.4 - - - -
132K LEU* 3.3 64.1 + - + +
134K VAL* 4.0 15.0 - - + -
143K TYR* 3.7 15.9 - - + +
144K VAL* 1.4 74.0 - - - +
146K ASN* 1.3 58.0 + - - +
154K ILE* 3.5 28.9 - - + -
155K TRP 3.7 4.3 - - - +
156K LEU* 3.6 20.6 - - + -
182K LEU* 4.6 6.1 - - + -
186K LEU* 4.3 13.7 - - + -
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Residues in contact with ASN 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K LEU* 4.6 3.4 - - - -
130K GLY 4.0 3.8 - - - -
131K VAL* 3.7 20.2 - - + -
144K VAL* 3.6 19.0 - - + +
145K ILE* 1.3 74.9 - - - +
147K LYS* 1.4 71.1 + - - +
148K GLN* 4.4 5.9 + - - -
154K ILE* 3.9 1.5 - - - -
155K TRP* 3.1 65.8 + - - +
157K SER* 4.7 0.9 - - - -
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Residues in contact with LYS 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K ALA* 3.8 30.1 - - + -
100K GLU* 4.6 19.7 + - + +
103K LEU* 3.9 12.8 - - + +
130K GLY* 3.3 33.9 + - - +
146K ASN* 1.4 81.0 + - - +
148K GLN* 1.4 71.7 + - - +
149K THR* 5.5 1.7 - - - +
152K LYS* 5.0 11.9 - - + +
153K GLN 3.8 6.7 - - - +
154K ILE* 4.4 4.0 - - - -
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Residues in contact with GLN 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ASN* 3.7 5.9 + - - +
147K LYS* 1.4 82.0 + - - +
149K THR* 1.3 91.1 + - - +
151K ASN* 4.2 16.6 - - + +
152K LYS* 3.4 22.1 - - - +
153K GLN* 2.9 36.8 + - + +
155K TRP* 3.3 41.9 - - + +
165K ARG* 5.3 8.1 - - + -
150L PRO* 5.1 10.8 - - + +
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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