Contacts of the strand formed by residues 131 - 139 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110G ARG* 4.3 8.5 - - - +
180G ILE 5.7 0.2 - - - -
181G ASN* 3.9 25.9 + - - -
215G THR* 5.6 10.3 - - - +
96I GLN* 3.5 27.0 + - + +
127I LEU* 3.4 4.5 - - - -
128I TYR 2.7 41.4 + - - +
129I ALA 3.3 8.3 + - - +
130I GLY* 1.3 79.7 - - - +
132I LYS* 1.3 67.8 + - - +
133I CYS* 4.0 5.7 - - - -
276K LYS* 2.6 46.8 - - - +
277K THR* 6.0 0.2 + - - -
280K ARG* 3.7 11.3 - - - +
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Residues in contact with LYS 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G GLY* 6.5 1.1 - - - -
52G LEU* 6.1 3.6 - - - +
106G GLU* 3.8 41.5 + - - +
110G ARG* 4.7 3.8 - - - +
96I GLN* 4.0 1.7 - - - +
97I ASP* 3.3 45.1 + - + +
102I ARG* 5.6 0.2 - - - +
125I GLU* 3.7 32.7 + - + +
126I ASN 3.6 9.6 - - - +
127I LEU* 4.3 14.1 - - + +
130I GLY 3.9 1.0 + - - -
131I ARG* 1.3 77.5 - - - +
133I CYS* 1.3 69.9 + - - +
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Residues in contact with CYS 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I MET* 4.3 13.7 - - + -
95I LEU 3.3 12.6 - - - +
96I GLN* 4.1 14.8 - - - -
97I ASP* 4.1 4.3 - - - +
124I TYR 3.4 3.8 - - - +
125I GLU* 3.4 4.2 - - - -
126I ASN 2.8 38.3 + - - +
128I TYR* 4.3 19.7 - - + -
131I ARG* 4.0 16.4 - - - -
132I LYS* 1.3 87.8 - - - +
134I LEU* 1.3 62.2 - - - +
135I LEU* 3.4 16.0 - - + +
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ILE* 4.4 6.1 - - + -
93I LYS 3.3 3.8 - - - +
95I LEU* 2.5 49.5 + - + +
97I ASP* 3.3 28.4 - - + +
101I ALA* 3.7 30.5 - - + +
102I ARG* 3.7 32.8 - - + +
105I VAL* 4.6 12.3 - - + -
123I VAL* 3.9 26.2 - - + -
124I TYR 3.5 6.3 - - - +
125I GLU* 4.9 4.5 - - + -
133I CYS* 1.3 71.2 - - - +
135I LEU* 1.3 63.4 + - - +
136I ILE* 3.9 1.9 + - + +
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Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G VAL* 5.3 7.6 - - + -
59I ILE* 3.9 28.0 - - + -
92I LEU* 3.7 22.7 - - + -
93I LYS 3.5 4.0 - - - -
94I MET* 3.9 24.5 - - - -
123I VAL* 3.3 3.7 - - - -
124I TYR* 2.7 54.1 + - + +
126I ASN* 4.5 13.0 - - + +
128I TYR* 6.1 2.2 - - + -
133I CYS* 3.4 31.0 - - + +
134I LEU* 1.3 82.2 - - - +
136I ILE* 1.3 62.1 + - - +
137I VAL* 3.9 1.0 + - - +
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Residues in contact with ILE 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I ALA 3.5 1.2 - - - +
92I LEU* 3.5 4.8 - - - +
93I LYS* 2.9 53.8 + - + +
95I LEU* 3.7 26.0 - - + -
104I GLU* 4.7 6.1 - - + +
105I VAL* 3.5 32.1 - - + +
108I HIS* 5.5 2.7 - - - +
120I ILE* 3.5 35.9 - - + -
122I ASP 3.7 2.2 - - - -
123I VAL* 4.3 9.4 - - + -
134I LEU 4.3 4.9 - - - +
135I LEU* 1.3 74.5 - - - +
137I VAL* 1.3 64.8 + - - +
138I MET* 3.7 11.5 + - + +
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Residues in contact with VAL 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I ILE* 3.7 29.6 - - + -
63I TYR* 3.8 30.1 - - + +
81I ILE* 4.0 13.2 - - + -
90I PHE* 4.1 11.2 - - + -
91I ALA 3.3 5.8 - - - +
92I LEU* 4.2 2.7 - - + -
120I ILE* 3.8 1.7 - - - -
121I VAL* 2.8 40.2 + - + -
122I ASP* 2.6 26.0 + - + +
124I TYR* 4.5 5.8 - - + -
135I LEU 3.9 0.2 + - - -
136I ILE* 1.3 73.6 - - - +
138I MET* 1.3 65.8 + - - +
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Residues in contact with MET 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I VAL* 4.1 17.0 - - + -
90I PHE* 3.1 21.8 - - - +
91I ALA* 2.9 28.3 + - + +
93I LYS* 3.7 39.3 - - + +
108I HIS* 4.4 4.7 - - + -
118I VAL* 4.4 16.2 - - + -
119I ARG 3.5 12.3 - - - +
120I ILE* 4.4 14.8 - - + -
121I VAL* 4.8 1.3 - - - -
136I ILE* 4.0 10.3 - - + +
137I VAL* 1.3 75.7 - - - +
139I GLU* 1.3 69.0 + - - +
500I MK2 3.4 37.9 - - + +
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Residues in contact with GLU 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I PHE* 4.0 12.6 - - + -
91I ALA* 4.2 1.4 - - - +
118I VAL* 4.0 7.9 - - + +
119I ARG* 3.0 60.2 + - - +
121I VAL* 4.6 2.7 - - + +
138I MET* 1.3 85.7 - - - +
140I CYS* 1.3 62.8 + - - +
141I LEU* 3.5 18.8 + - + +
195I THR* 5.1 2.8 - - - +
204I LYS* 2.8 37.0 + - - +
500I MK2 3.6 10.6 + - - -
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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