Contacts of the strand formed by residues 131 - 139 (chain K) in PDB entry 3KC3
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 131 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273I PRO* 3.3 47.1 + - + +
276I LYS* 5.7 6.1 - - - +
277I THR* 3.5 9.7 + - - -
280I ARG* 5.4 5.4 - - - +
96K GLN* 3.3 36.2 + - + +
127K LEU* 3.4 4.6 - - - -
128K TYR* 2.8 32.1 + - + +
129K ALA* 2.7 33.4 + - - +
130K GLY* 1.3 76.2 - - - +
132K LYS* 1.3 68.3 + - - +
133K CYS* 3.5 3.8 + - - -
110L ARG* 4.7 4.5 - - - +
179L SER 4.1 5.3 + - - -
180L ILE* 4.1 17.4 + - - +
181L ASN* 3.8 22.5 + - - -
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Residues in contact with LYS 132 (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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96K GLN* 3.9 6.8 - - - +
97K ASP* 3.4 39.0 + - + +
102K ARG* 5.3 1.8 - - - +
125K GLU* 3.2 37.2 + - + +
126K ASN 3.7 4.3 - - - +
127K LEU* 4.0 11.5 - - + +
130K GLY 4.2 0.8 + - - -
131K ARG* 1.3 75.0 - - - +
133K CYS* 1.3 64.1 + - - +
106L GLU* 3.2 42.7 + - + +
110L ARG* 4.9 9.2 - - - +
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Residues in contact with CYS 133 (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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94K MET* 4.9 11.0 - - + -
95K LEU 3.6 11.2 - - - +
96K GLN* 4.5 11.2 - - - -
97K ASP* 4.3 2.4 - - - +
124K TYR 3.4 0.7 - - - +
125K GLU* 3.3 7.0 - - - +
126K ASN* 2.6 48.5 + - + +
128K TYR* 3.6 27.6 - - + -
131K ARG* 3.6 11.2 - - - -
132K LYS* 1.3 85.1 - - - +
134K LEU* 1.3 66.2 + - - +
135K LEU* 3.8 9.9 + - + -
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Residues in contact with LEU 134 (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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54K ILE* 5.5 1.8 - - + -
93K LYS 4.0 0.7 - - - +
94K MET* 3.7 1.6 - - - +
95K LEU* 2.8 50.5 + - + +
97K ASP* 3.9 15.3 - - + +
101K ALA* 4.0 22.7 - - + +
102K ARG* 3.8 32.8 - - - +
105K VAL* 3.8 30.5 - - + -
123K VAL* 4.9 8.1 - - + -
124K TYR 3.2 7.6 - - - +
125K GLU* 3.7 28.5 - - + -
133K CYS* 1.3 73.2 - - - +
135K LEU* 1.3 61.1 + - - +
136K ILE* 4.0 3.8 + - + +
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Residues in contact with LEU 135 (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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59K ILE* 3.8 25.1 - - + -
92K LEU* 3.7 24.2 - - + -
93K LYS 3.7 1.3 - - - -
94K MET* 3.4 45.1 - - + -
123K VAL* 3.5 2.8 - - - -
124K TYR* 2.7 41.4 + - + +
126K ASN* 3.5 39.0 - - + +
128K TYR* 6.5 0.4 - - + -
133K CYS* 4.6 6.5 - - + +
134K LEU* 1.3 73.0 - - - +
136K ILE* 1.3 62.4 + - - +
137K VAL* 3.6 1.8 + - - +
48L VAL* 4.7 7.4 - - + -
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Residues in contact with ILE 136 (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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91K ALA 3.6 0.2 - - - +
92K LEU* 3.5 3.4 - - - -
93K LYS* 2.8 49.5 + - + +
95K LEU* 3.9 17.0 - - + -
104K GLU* 3.8 22.4 - - - +
105K VAL* 4.0 26.5 - - + -
108K HIS* 5.3 4.9 - - + +
120K ILE* 3.5 41.5 - - + -
122K ASP 3.8 1.3 - - - -
123K VAL* 4.2 9.6 - - + +
134K LEU* 4.9 3.4 - - + +
135K LEU* 1.3 72.4 - - - +
137K VAL* 1.3 65.0 + - - +
138K MET* 3.6 9.2 + - + +
500K MK2 6.2 0.4 - - - +
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Residues in contact with VAL 137 (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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59K ILE* 3.7 30.7 - - + -
63K TYR* 3.6 31.6 - - + +
81K ILE* 4.0 18.2 - - + -
90K PHE* 4.1 9.9 - - + -
91K ALA 3.5 2.9 - - - -
92K LEU* 4.2 1.8 - - + -
120K ILE* 3.8 2.9 - - - +
121K VAL* 2.8 40.8 + - + -
122K ASP* 2.6 23.7 + - + +
124K TYR* 4.0 14.4 - - + -
136K ILE* 1.3 73.6 - - - +
138K MET* 1.3 55.5 + - - +
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Residues in contact with MET 138 (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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78K VAL* 4.2 17.5 - - + -
90K PHE* 3.3 10.6 - - - +
91K ALA* 2.6 43.9 + - + +
93K LYS* 4.0 26.9 - - + +
108K HIS* 4.1 9.6 - - + -
118K VAL* 4.3 6.3 - - + -
119K ARG 3.6 13.0 - - - +
120K ILE* 4.3 15.5 - - + -
121K VAL* 4.2 4.3 - - - -
136K ILE* 4.3 7.0 - - + +
137K VAL* 1.3 75.5 - - - +
139K GLU* 1.3 64.9 + - - +
206K THR* 4.3 7.0 - - - -
500K MK2 3.2 44.2 - - + +
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Residues in contact with GLU 139 (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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90K PHE* 4.1 11.4 - - + -
91K ALA* 4.3 0.6 - - - +
118K VAL* 3.5 9.7 - - + +
119K ARG* 2.9 61.4 + - - +
121K VAL* 3.9 6.0 - - + +
138K MET* 1.3 78.3 - - - +
140K CYS* 1.3 62.9 + - - +
141K LEU* 3.6 16.9 + - + +
204K LYS* 3.0 36.2 + - - +
500K MK2 3.7 11.8 + - - -
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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