Contacts of the strand formed by residues 131 - 139 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B GLN* 3.2 38.3 + - + +
127B LEU* 3.7 2.1 - - - -
128B TYR 2.8 35.2 + - - +
129B ALA* 2.5 16.9 + - + +
130B GLY* 1.3 72.4 - - - +
132B LYS* 1.3 61.5 + - - +
133B CYS* 3.8 9.2 + - - -
110C ARG* 4.2 5.2 - - - +
181C ASN* 4.7 12.9 + - - -
273L PRO* 4.5 30.6 + - + +
276L LYS* 4.8 14.1 - - - +
277L THR* 5.2 3.2 + - - -
280L ARG* 4.0 30.8 - - - +
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Residues in contact with LYS 132 (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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96B GLN* 4.0 2.3 - - - +
97B ASP* 3.2 51.1 + - + +
102B ARG* 5.0 1.8 - - - +
125B GLU* 3.2 30.9 + - + +
126B ASN 3.7 7.9 - - - +
127B LEU* 4.1 15.4 - - + +
130B GLY 4.0 1.6 + - - -
131B ARG* 1.3 73.0 - - - +
133B CYS* 1.3 65.2 + - - +
51C GLY* 6.2 0.9 - - - -
52C LEU* 5.8 4.1 - - - +
106C GLU* 3.7 38.5 + - - +
109C TRP* 5.9 6.1 - - - -
110C ARG* 4.7 14.9 - - - +
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Residues in contact with CYS 133 (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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94B MET* 5.0 7.2 - - + -
95B LEU 3.6 13.2 - - - +
96B GLN* 4.0 16.6 - - - -
97B ASP* 4.3 1.8 - - - +
124B TYR 3.5 1.0 - - - +
125B GLU* 3.2 7.6 - - - +
126B ASN 2.5 47.2 + - - +
128B TYR* 4.4 22.9 - - + -
131B ARG* 3.8 14.8 - - - +
132B LYS* 1.3 83.5 - - - +
134B LEU* 1.3 63.4 + - - +
135B LEU* 3.7 15.7 - - + +
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Residues in contact with LEU 134 (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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54B ILE* 4.8 5.2 - - + -
93B LYS 3.8 0.7 - - - +
94B MET* 3.6 0.3 - - - -
95B LEU* 2.8 48.7 + - + +
97B ASP* 4.2 12.7 - - - +
101B ALA* 3.8 25.6 - - + +
102B ARG* 3.8 42.6 - - + +
105B VAL* 3.8 31.4 - - + -
123B VAL* 4.7 8.5 - - + -
124B TYR 3.4 9.0 - - - +
125B GLU* 4.2 7.9 - - + -
133B CYS* 1.3 77.0 - - - +
135B LEU* 1.3 65.9 + - - +
136B ILE* 3.9 0.8 + - - -
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Residues in contact with LEU 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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59B ILE* 3.8 28.5 - - + -
92B LEU* 3.3 30.3 - - + -
93B LYS 3.3 4.7 - - - +
94B MET* 4.6 17.9 - - + -
122B ASP 4.1 0.2 - - - +
123B VAL* 3.4 3.9 - - - -
124B TYR* 2.9 47.1 + - + +
126B ASN* 4.6 10.5 - - + +
128B TYR* 6.1 0.7 - - + -
133B CYS* 3.7 27.8 - - + +
134B LEU* 1.3 83.1 - - - +
136B ILE* 1.3 61.7 + - - +
137B VAL* 3.7 1.2 + - - +
48C VAL* 4.8 9.9 - - + -
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Residues in contact with ILE 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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91B ALA 3.7 0.7 - - - +
92B LEU* 3.5 5.4 - - - +
93B LYS* 2.9 41.3 + - + +
95B LEU* 3.7 28.7 - - + -
104B GLU* 4.3 12.1 - - + +
105B VAL* 3.8 28.0 - - + -
108B HIS* 5.0 7.2 - - - +
120B ILE* 3.6 33.7 - - + -
122B ASP 3.9 3.1 - - - -
123B VAL* 4.5 6.1 - - + -
134B LEU 5.3 0.4 - - - -
135B LEU* 1.3 74.2 - - - +
137B VAL* 1.3 61.3 + - - +
138B MET* 3.8 22.7 + - + +
500B MK2 6.1 0.2 - - - +
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Residues in contact with VAL 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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59B ILE* 3.6 31.4 - - + -
63B TYR* 3.8 22.4 - - + +
81B ILE* 4.1 10.3 - - + -
90B PHE* 4.0 19.3 - - + -
91B ALA 3.4 9.0 - - - +
92B LEU* 4.3 1.8 - - + -
120B ILE* 3.6 2.6 - - - +
121B VAL* 2.6 40.8 + - + -
122B ASP* 2.8 24.8 + - + +
124B TYR* 4.2 13.9 - - + -
135B LEU 4.5 0.4 - - - +
136B ILE* 1.3 75.5 - - - +
138B MET* 1.3 53.9 + - - +
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Residues in contact with MET 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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78B VAL* 4.1 15.0 - - + -
90B PHE* 3.7 6.8 - - - -
91B ALA* 2.8 54.3 + - + +
93B LYS* 4.1 21.1 - - + +
108B HIS* 4.1 14.4 - - + -
118B VAL* 3.8 14.4 - - + -
119B ARG 3.3 13.9 - - - +
120B ILE* 4.6 0.9 - - + -
121B VAL* 4.2 4.7 - - - -
136B ILE* 3.9 15.0 - - + +
137B VAL* 1.3 75.6 - - - +
139B GLU* 1.3 74.2 + - - +
140B CYS 3.5 0.2 + - - -
206B THR* 4.5 0.4 - - - -
500B MK2 3.6 37.5 - - + +
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Residues in contact with GLU 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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90B PHE* 4.4 10.1 - - + -
91B ALA* 3.7 0.5 - - - +
118B VAL* 3.4 4.5 - - + -
119B ARG* 2.8 60.6 + - + +
121B VAL* 4.0 3.7 - - - +
138B MET* 1.3 77.2 - - - +
140B CYS* 1.3 60.3 + - - +
141B LEU* 3.4 22.0 - - + +
195B THR* 4.7 3.1 - - - +
204B LYS* 2.8 37.5 + - - -
500B MK2 3.1 21.1 + - - -
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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