Contacts of the strand formed by residues 134 - 144 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.4 4.9 - - - -
66A LYS* 3.5 13.8 - - + +
68A GLY* 3.8 20.9 - - - -
131A HIS* 2.8 32.2 + - + +
133A ASN* 1.3 80.3 - - - +
135A ALA* 1.3 59.9 + - - +
136A CYS 3.4 7.6 - - - +
174A LEU* 5.0 0.4 - - + -
177A LYS* 2.6 31.9 + - - +
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Residues in contact with ALA 135 (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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61A ASN 4.7 5.0 - - - +
62A MET* 4.0 26.0 - - + +
64A PHE* 3.6 23.6 - - + -
66A LYS 3.0 9.8 + - - +
67A LEU* 3.0 15.6 + - - +
134A ALA* 1.3 74.3 - - - +
136A CYS* 1.3 63.2 + - - +
177A LYS* 3.6 21.1 - - - +
178A PRO* 3.8 6.2 - - - +
303A GLN* 4.0 10.3 - - - +
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Residues in contact with CYS 136 (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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62A MET* 4.9 4.3 - - + -
67A LEU* 2.8 36.0 + - - -
68A GLY* 3.2 21.0 - - - -
69A LYS 3.9 1.2 + - - -
106A PHE* 3.7 18.4 - - - -
131A HIS* 5.5 0.9 + - - -
134A ALA* 3.4 7.4 - - - +
135A ALA* 1.3 79.1 - - - +
137A PHE* 1.3 63.3 + - - +
174A LEU* 4.1 11.2 - - - +
177A LYS* 4.5 1.3 - - - -
178A PRO* 3.1 32.8 - - + +
180A LEU* 4.5 10.1 - - - -
299A LEU* 5.6 0.4 - - - -
301A PHE* 5.0 2.0 - - - -
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Residues in contact with PHE 137 (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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69A LYS* 3.8 24.0 - - + -
71A ILE* 4.2 20.0 - - + -
106A PHE* 4.6 0.2 - - - -
123A LEU* 4.8 1.6 - - + -
126A ALA* 4.3 13.2 - - + -
131A HIS* 4.8 7.6 - + - +
136A CYS* 1.3 79.4 - - - +
138A ALA* 1.3 71.4 + - - +
139A CYS* 3.9 24.9 - - + -
166A PHE* 3.5 46.7 - + - -
174A LEU* 3.6 22.4 - - + -
178A PRO 3.1 5.7 + - - +
179A LYS* 3.5 15.1 - - + -
180A LEU* 2.7 33.9 + - - +
181A PHE* 4.2 7.9 - + - -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LYS 2.9 8.9 + - - +
70A CYS* 3.0 16.8 - - - -
71A ILE 2.9 22.5 + - - -
101A PHE* 4.6 1.6 - - + -
106A PHE* 3.8 29.2 - - + -
137A PHE* 1.3 83.4 - - - +
139A CYS* 1.3 60.4 + - - +
140A ILE* 5.6 0.2 - - + -
180A LEU* 3.1 19.1 - - + +
182A PHE* 4.4 9.4 - - + -
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Residues in contact with CYS 139 (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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71A ILE* 3.4 15.7 - - + +
123A LEU* 4.0 25.4 - - - -
137A PHE* 3.9 11.6 - - + -
138A ALA* 1.3 75.5 - - - +
140A ILE* 1.3 66.2 + - - +
141A LEU* 3.7 30.6 - - - +
180A LEU 2.7 5.9 + - - +
181A PHE* 3.3 28.5 - - + -
182A PHE* 2.9 25.5 + - - +
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A CYS* 3.9 18.2 - - - -
71A ILE 2.7 12.5 + - - +
72A ILE* 4.1 14.8 - - + +
73A ILE 2.9 28.1 + - - +
97A LEU* 3.6 33.7 - - + -
101A PHE* 3.7 39.9 - - + -
138A ALA 5.3 0.2 - - - -
139A CYS* 1.3 79.0 - - - +
141A LEU* 1.3 64.2 + - - +
142A LEU* 3.8 14.4 - - + -
182A PHE* 3.3 26.2 - - + +
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Residues in contact with LEU 141 (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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73A ILE* 3.4 39.7 - - + -
119A MET* 5.3 3.6 - - - -
123A LEU* 5.2 0.4 - - + -
139A CYS* 3.7 22.2 - - - -
140A ILE* 1.3 71.9 - - - +
142A LEU* 1.3 64.3 + - - +
143A SER* 4.0 1.8 - - - -
150A ILE* 4.4 16.6 - - + -
159A ILE* 5.3 2.7 - - + -
162A LEU* 3.6 31.2 - - + -
181A PHE* 5.3 5.6 - - + -
182A PHE 2.8 9.5 + - - +
183A ILE* 3.6 32.2 - - + +
184A GLN 2.9 28.4 + - - +
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Residues in contact with LEU 142 (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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72A ILE* 4.6 6.7 - - + -
73A ILE* 2.9 16.5 + - - +
74A ASN* 4.3 4.0 - - + -
75A ASN 2.9 28.1 + - - +
87A ARG* 3.7 7.5 + - - +
90A THR* 3.9 20.9 - - - +
93A ASP* 4.3 5.4 - - + -
94A ALA* 4.0 35.9 - - + +
97A LEU* 3.8 15.7 - - + -
140A ILE* 3.8 20.2 - - + +
141A LEU* 1.3 83.1 - - - +
143A SER* 1.3 61.6 + - - +
184A GLN* 3.7 24.5 - - + -
242A VAL* 4.9 4.3 - - + -
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Residues in contact with SER 143 (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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73A ILE* 6.1 0.4 - - - -
75A ASN* 3.5 12.0 - - - +
78A PHE* 3.3 12.8 - - - -
87A ARG* 3.2 24.1 + - - +
119A MET* 6.0 0.2 - - - -
141A LEU* 4.0 1.9 - - - -
142A LEU* 1.3 77.0 - - - +
144A HIS* 1.3 73.6 + - - +
150A ILE* 4.7 9.1 - - - +
151A TYR 2.7 29.5 + - - -
184A GLN 3.2 8.7 + - - +
185A ALA* 3.1 19.9 - - - +
186A CYS 3.4 4.0 + - - -
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Residues in contact with HIS 144 (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 PHE* 3.3 26.2 - + - -
84A MET* 3.2 44.3 - - + +
85A GLY* 2.8 30.5 + - - -
86A VAL 5.4 0.2 - - - -
87A ARG* 3.4 21.2 - - + +
143A SER* 1.3 81.6 + - - +
145A GLY* 1.3 58.7 + - - +
150A ILE* 3.6 3.5 - - - +
151A TYR* 2.8 36.6 + - + -
185A ALA* 4.1 1.3 - - - -
186A CYS* 3.7 20.3 + - - +
187A ARG* 4.4 12.2 - - - +
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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