Contacts of the strand formed by residues 120 - 128 (chain H) 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 ILE 120 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105H VAL* 4.5 4.9 - - - +
108H HIS* 3.2 63.5 - - + +
109H TRP* 3.6 32.1 - - + +
112H SER* 3.6 13.6 + - - +
119H ARG* 1.3 80.0 + - - +
121H VAL* 1.3 63.4 + - - +
122H ASP 4.2 6.1 - - - +
123H VAL* 3.8 27.8 - - + -
136H ILE* 3.9 25.1 - - + -
137H VAL 3.8 5.6 - - - +
138H MET* 4.3 1.1 - - + -
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H TYR* 3.9 20.6 - - - +
90H PHE* 3.6 27.6 - - + -
109H TRP* 5.3 3.7 - - - -
119H ARG* 3.3 34.3 + - - +
120H ILE* 1.3 75.6 - - - +
122H ASP* 1.3 74.1 + - - +
137H VAL* 2.6 20.7 + - + +
139H GLU* 4.1 11.4 - - - +
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Residues in contact with ASP 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLN 5.7 0.5 - - - +
55H LYS* 2.9 39.2 + - + +
63H TYR* 3.8 14.0 + - - +
85H ARG* 5.2 5.7 + - - -
109H TRP* 6.1 1.3 - - - -
120H ILE* 3.7 3.1 - - - +
121H VAL* 1.3 93.3 - - + +
123H VAL* 1.3 65.4 + - - +
124H TYR* 3.7 22.7 + - + -
135H LEU 3.7 1.4 - - - +
137H VAL* 2.9 33.2 + - + +
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Residues in contact with VAL 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LEU* 3.3 32.9 - - + +
53H GLN 4.6 0.4 + - - +
54H ILE* 3.0 37.1 - - + +
55H LYS* 3.0 14.6 + - - +
105H VAL* 3.8 31.0 - - + -
109H TRP* 5.4 0.4 - - + -
120H ILE* 3.8 17.7 - - + -
122H ASP* 1.3 78.4 + - - +
124H TYR* 1.3 67.8 + - - +
134H LEU* 4.4 8.7 - - + -
135H LEU 3.7 7.6 - - - +
136H ILE* 5.0 5.4 - - + -
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Residues in contact with TYR 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ILE* 3.7 2.7 - - - -
55H LYS* 3.2 38.3 - - + -
57H ASN* 3.3 34.5 - - - -
59H ILE* 3.7 37.2 - - + -
62H ASP* 2.7 22.6 + - - -
63H TYR* 3.3 22.5 - + - -
85H ARG* 5.6 0.9 + - - -
122H ASP* 3.7 20.9 + - + -
123H VAL* 1.3 78.2 - - - +
125H GLU* 1.3 59.7 + - - +
126H ASN* 3.9 11.7 - - - +
133H CYS 3.4 0.3 - - - +
134H LEU* 3.4 5.5 - - - +
135H LEU* 2.9 47.4 + - + +
137H VAL* 4.1 3.1 - - + -
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H ILE* 3.5 14.0 - - + +
55H LYS 2.7 9.5 + - - -
56H LYS* 3.0 44.6 - - + +
97H ASP* 4.0 6.5 - - - +
124H TYR* 1.3 71.6 - - - +
126H ASN* 1.3 70.8 + - - +
132H LYS* 3.6 41.6 + - + +
133H CYS 3.3 9.2 - - - +
134H LEU* 4.7 12.9 - - + +
51I GLY* 3.2 20.4 + - - -
52I LEU* 4.4 7.6 + - - +
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Residues in contact with ASN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H LYS 3.4 4.9 + - - -
57H ASN 3.1 21.6 + - - -
58H ALA* 3.1 6.9 - - - -
59H ILE* 2.6 32.9 + - - +
124H TYR* 3.9 8.6 - - - +
125H GLU* 1.3 94.4 + - - +
127H LEU* 1.3 59.9 + - - +
128H TYR* 4.0 0.4 - - + -
132H LYS* 3.9 2.6 - - - +
133H CYS* 2.7 41.0 + - + +
135H LEU* 4.5 10.3 - - + -
48I VAL* 3.5 19.3 - - + +
49I LYS 3.5 8.5 - - - +
51I GLY* 4.0 4.5 - - - +
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Residues in contact with LEU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ASN* 1.3 73.1 - - - +
128H TYR* 1.3 60.2 + - - +
129H ALA 4.1 0.4 + - - -
130H GLY* 3.9 25.1 - - - +
131H ARG 3.6 8.7 - - - +
132H LYS* 4.4 9.6 - - + +
47I HIS 3.4 4.9 - - - +
48I VAL* 3.8 1.4 - - - +
49I LYS* 2.8 39.3 + - + +
50I SER 3.7 14.3 + - - +
51I GLY* 5.1 0.7 - - - +
109I TRP* 4.1 26.7 - - + +
110I ARG* 4.3 28.5 - - + +
113I GLN* 3.7 27.8 - - + +
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Residues in contact with TYR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H MET* 6.4 3.4 - - - -
126H ASN* 4.0 0.8 - - + -
127H LEU* 1.3 73.9 - - - +
129H ALA* 1.3 85.1 + - + +
131H ARG* 2.8 26.8 + - - +
133H CYS* 3.7 26.5 - - + -
135H LEU* 6.0 2.0 - - + -
46I PHE 4.1 15.3 - - - -
47I HIS* 3.9 12.3 - - + +
48I VAL* 3.8 24.5 - - + -
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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