Contacts of the strand formed by residues 123 - 128 (chain C) in PDB entry 3KHU
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 TYR 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C PHE* 3.8 47.4 - + + -
82C ALA 4.7 1.6 - - - +
83C ASP* 4.6 7.3 - - - +
121C ASN 3.6 1.1 + - - +
122C GLY* 1.3 69.4 - - - -
124C LYS* 1.3 72.7 + - - +
125C ILE* 3.6 29.2 - - + +
153C ASN* 3.3 32.1 - - + -
155C GLN* 3.8 15.1 - - + +
187C GLU* 3.6 25.4 + - - -
190C ARG* 4.6 14.8 - - - +
191C ALA* 4.0 12.5 + - - +
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Residues in contact with LYS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ILE 3.2 18.4 - - - +
80C LYS 3.0 22.5 + - - -
81C GLU 4.4 0.8 - - - -
82C ALA 2.7 28.4 + - - +
83C ASP 3.4 9.9 - - - +
85C VAL* 4.2 13.2 - - + -
116C ILE* 5.4 0.7 - - + -
120C SER* 3.4 35.7 - - - +
121C ASN 4.1 13.6 + - - +
122C GLY 3.9 0.8 + - - -
123C TYR* 1.3 83.0 + - - +
125C ILE* 1.3 67.8 + - - +
126C VAL* 4.9 1.8 - - + -
153C ASN 3.2 6.8 + - - +
154C LEU* 3.4 18.1 - - + +
155C GLN* 3.0 26.5 + - - +
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Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PHE* 4.2 10.5 - - + -
4C ILE* 4.1 15.3 - - + -
83C ASP 2.9 9.2 + - - +
84C LEU* 3.2 22.4 - - + +
85C VAL* 2.7 32.6 + - - +
123C TYR* 3.6 27.4 - - + +
124C LYS* 1.3 73.6 - - - +
126C VAL* 1.3 56.5 - - - +
127C THR* 3.7 2.5 - - - +
155C GLN* 3.6 5.8 - - + +
157C LEU* 3.5 30.7 - - + -
191C ALA* 3.9 15.7 - - + +
194C ALA* 3.8 28.0 - - + -
195C LEU 5.1 0.2 - - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C VAL* 3.3 12.8 - - + +
87C ILE* 3.9 17.0 - - + -
116C ILE* 3.9 37.7 - - + -
124C LYS* 4.9 0.7 - - + -
125C ILE* 1.3 76.5 - - - +
127C THR* 1.3 63.9 + - - +
140C ILE* 4.7 6.5 - - + -
144C PHE* 3.9 31.9 - - + -
154C LEU* 4.2 13.7 - - + -
155C GLN 2.7 14.4 + - - +
156C VAL* 3.3 6.9 - - - +
157C LEU 2.9 23.6 + - - +
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Residues in contact with THR 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 3.2 22.2 - - - +
85C VAL 2.9 9.1 + - - -
86C PHE* 3.4 26.8 - - + -
87C ILE* 2.9 29.6 + - - -
125C ILE* 3.7 7.1 - - - +
126C VAL* 1.3 74.3 + - - +
128C GLU* 1.3 63.9 + - - +
129C LYS 3.4 0.2 + - - -
157C LEU* 3.3 17.2 - - + +
159C ASN* 3.4 34.8 - - + +
195C LEU* 4.0 6.9 - - + +
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ILE* 3.8 10.1 - - + +
109C ILE* 5.8 1.8 - - + -
126C VAL* 4.3 0.8 - - - +
127C THR* 1.3 71.0 - - - +
129C LYS* 1.3 58.4 + - - +
130C SER 4.5 2.2 - - - +
132C VAL* 3.7 21.7 - - + +
136C ALA* 3.0 17.0 - - - +
137C ALA* 2.9 31.6 + - + +
140C ILE* 3.7 21.5 - - + +
156C VAL* 5.2 0.9 - - + -
157C LEU 3.0 11.5 + - - +
158C SER* 3.5 20.6 + - - +
159C ASN* 2.9 31.7 + - - +
160C PRO* 4.8 0.3 - - - +
217C GLU* 2.8 23.3 - - - +
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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