Contacts of the strand formed by residues 134 - 146 (chain B) in PDB entry 1K86
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 ALA 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B PHE* 3.6 5.2 - - - -
66B LYS* 3.1 11.2 - - + +
68B GLY* 3.6 25.6 - - - +
131B HIS* 2.8 25.1 + - + +
133B ASN* 1.3 81.9 - - - +
135B ALA* 1.3 64.7 + - - +
136B CYS 4.0 6.5 - - - +
174B LEU* 5.3 0.4 - - + -
177B LYS* 2.8 25.8 + - - +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN 5.0 1.9 - - - +
62B MET* 3.7 41.2 - - + +
64B PHE* 3.6 23.1 - - + +
66B LYS 2.9 12.6 + - - +
67B LEU* 3.2 12.0 + - - +
134B ALA* 1.3 71.9 - - - +
136B CYS* 1.3 61.0 + - - +
177B LYS* 3.4 25.5 - - - +
178B PRO* 3.9 6.1 - - - +
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B MET* 4.6 6.1 - - + -
67B LEU* 2.9 36.2 + - - -
68B GLY* 3.3 21.8 - - - -
69B LYS 3.9 0.7 + - - -
106B PHE* 3.6 18.4 - - - -
131B HIS* 5.5 1.0 + - - -
134B ALA* 3.5 6.6 - - - +
135B ALA* 1.3 76.5 - - + +
137B PHE* 1.3 64.8 + - - +
174B LEU* 4.3 5.9 - - - +
177B LYS* 4.5 4.3 - - - -
178B PRO* 3.1 34.8 - - + +
180B LEU* 4.5 9.2 - - + -
299B LEU* 5.5 0.4 - - - -
301B PHE* 4.8 2.5 - - - -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 3.6 29.6 - - + -
71B ILE* 4.1 26.9 - - + -
106B PHE* 4.6 1.8 - - - -
123B LEU* 4.9 0.9 - - + -
126B ALA* 4.8 2.5 - - + -
131B HIS* 4.6 10.3 - + - +
136B CYS* 1.3 81.0 - - - +
138B ALA* 1.3 67.9 + - - +
139B CYS* 3.8 25.1 - - + -
166B PHE* 3.6 44.6 - + - -
174B LEU* 3.7 22.7 - - + -
178B PRO 3.1 5.7 + - - +
179B LYS* 3.5 7.0 - - + -
180B LEU* 2.7 35.3 + - - +
181B PHE* 4.2 11.0 - + - -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS 2.9 9.8 + - - +
70B CYS* 3.3 7.6 - - - -
71B ILE 3.0 22.3 + - - -
101B PHE* 4.1 19.3 - - + -
106B PHE* 3.6 28.0 - - + -
137B PHE* 1.3 84.3 - - - +
139B CYS* 1.3 61.1 + - - +
180B LEU* 3.2 15.0 - - + +
182B PHE* 4.3 2.9 - - + -
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Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 3.3 11.7 - - + +
123B LEU* 4.3 15.7 - - - -
137B PHE* 3.8 12.8 - - + -
138B ALA* 1.3 77.9 - - - +
140B ILE* 1.3 68.2 + - - +
141B LEU* 3.8 29.6 - - - -
180B LEU 2.7 8.7 + - - -
181B PHE* 3.3 37.8 - - + +
182B PHE* 2.8 26.9 + - - +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B CYS* 3.9 24.9 - - - -
71B ILE 2.7 11.7 + - - +
72B ILE* 3.3 20.7 - - + +
73B ILE* 2.7 33.4 + - - +
97B LEU* 3.9 20.0 - - + -
101B PHE* 4.0 28.7 - - + -
139B CYS* 1.3 79.9 - - - +
141B LEU* 1.3 61.0 + - - +
142B LEU* 3.7 26.2 - - + -
182B PHE* 3.2 28.3 - - + +
184B GLN* 6.1 0.2 - - + -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ILE* 3.5 37.0 - - + -
119B MET* 5.5 1.1 - - - -
123B LEU* 5.1 1.6 - - + -
139B CYS* 3.8 22.7 - - - -
140B ILE* 1.3 71.5 - - - +
142B LEU* 1.3 63.2 + - - +
143B SER 3.9 1.1 + - - -
150B ILE* 3.6 30.2 - - + +
159B ILE* 5.0 6.7 - - + -
162B LEU* 4.1 22.2 - - + -
163B THR* 5.6 1.1 - - + -
181B PHE* 5.4 4.5 - - + -
182B PHE 3.0 9.9 + - - +
183B ILE* 3.7 28.6 - - + +
184B GLN 2.9 29.3 + - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 4.3 9.0 - - + -
73B ILE* 2.8 15.8 + - - +
74B ASN* 4.0 7.9 - - - +
75B ASN* 2.7 29.6 + - - +
87B ARG* 3.4 11.8 + - - +
90B THR* 3.8 13.9 - - - +
93B ASP* 4.3 4.5 - - + +
94B ALA* 3.9 39.5 - - + +
97B LEU* 3.9 15.7 - - + -
140B ILE* 3.7 20.6 - - + -
141B LEU* 1.3 81.2 - - - +
143B SER* 1.3 58.6 + - - +
184B GLN* 3.5 25.4 - - + -
242B VAL* 4.6 3.6 - - + -
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ILE* 5.8 0.2 - - - -
75B ASN* 3.5 13.2 - - - -
78B PHE* 3.3 11.6 - - - -
87B ARG* 3.4 24.6 + - - +
141B LEU 3.9 0.8 - - - -
142B LEU* 1.3 75.9 - - - +
144B HIS* 1.3 70.2 + - - +
150B ILE* 3.9 16.8 - - - -
151B TYR 2.6 30.9 + - - -
184B GLN 3.3 5.9 + - - +
185B ALA* 3.2 23.2 - - - +
186B CYS 3.6 1.7 + - - -
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Residues in contact with HIS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE* 3.4 26.9 - + - -
84B MET* 3.3 44.1 - - + +
85B GLY 2.9 27.1 + - - -
86B VAL 5.4 0.4 - - - -
87B ARG* 3.4 19.3 + - + +
143B SER* 1.3 82.9 + - - +
145B GLY* 1.3 58.9 + - - +
150B ILE* 3.5 3.8 - - - +
151B TYR* 2.7 36.6 + - + -
185B ALA* 4.0 0.7 - - - -
186B CYS* 3.3 14.3 + - + +
187B ARG 3.6 13.6 + - - -
188B GLY* 5.6 1.3 - - - -
230B TYR* 6.3 0.9 - + - -
233B ARG* 6.1 2.7 - - - -
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B HIS* 1.3 75.9 - - - +
146B GLU* 1.3 72.1 + - - +
149B VAL 3.5 11.9 - - - -
150B ILE* 4.4 0.2 - - - -
151B TYR* 3.9 4.5 - - - -
185B ALA* 3.8 16.8 - - - -
186B CYS* 2.6 32.8 + - - +
187B ARG* 3.3 6.0 - - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET* 4.1 5.9 - - - +
145B GLY* 1.3 82.4 - - - +
147B GLU* 1.3 73.0 + - + +
148B ASN 2.7 1.4 + - - -
149B VAL* 2.7 31.9 + - + +
151B TYR* 2.7 34.1 + - + -
156B VAL* 5.2 1.0 - - - +
159B ILE* 5.5 0.2 - - - +
187B ARG* 3.7 35.6 - - + +
188B GLY 5.8 0.3 + - - -
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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