Contacts of the strand formed by residues 111 - 116 (chain C) in PDB entry 3K9L
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 MET 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 3.1 24.9 - - + -
80C CYS* 3.1 31.6 - - + -
93C ILE* 5.8 1.1 - - + -
97C ARG* 4.0 36.1 - - + +
100C ILE* 4.2 16.8 - - - -
101C LYS* 6.2 1.1 - - - -
109C VAL* 3.2 17.8 + - + +
110C PRO* 1.3 81.2 - - - +
112C VAL* 1.3 69.4 + - - +
137C TYR* 5.2 1.6 - - + -
139C ILE* 3.4 44.8 - - + +
140C PRO* 3.5 5.2 - - - +
159C LEU* 3.9 3.2 - - - +
162C GLU* 4.3 5.2 + - - +
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Residues in contact with VAL 112 (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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78C PHE 3.0 6.3 + - - +
79C LEU* 3.8 15.0 - - + -
80C CYS* 2.9 27.1 + - - +
111C MET* 1.3 80.3 - - - +
113C LEU* 1.3 75.2 + - - +
114C VAL* 3.7 10.5 + - + +
139C ILE* 4.1 4.3 - - - -
140C PRO* 3.7 26.0 - - + +
142C ILE* 3.7 23.8 - - + -
155C ALA 4.4 2.5 - - - +
158C THR* 4.0 4.7 - - + -
159C LEU* 3.8 32.3 - - + +
162C GLU* 4.2 2.0 - - + -
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Residues in contact with LEU 113 (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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80C CYS* 3.6 16.6 - - + +
82C PHE* 3.7 24.0 - - + -
93C ILE* 4.0 26.9 - - + -
112C VAL* 1.3 74.3 - - - +
114C VAL* 1.3 59.8 + - - +
130C ALA* 3.4 27.4 - - + +
133C LEU* 4.2 12.3 - - + -
134C ALA* 3.8 14.8 - - + +
137C TYR* 5.8 0.7 - - + -
139C ILE* 3.8 14.5 - - + +
140C PRO 2.9 14.1 + - - +
141C TYR* 3.3 20.1 - - + -
142C ILE 2.8 25.6 + - - -
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Residues in contact with VAL 114 (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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19C LEU* 4.2 14.8 - - + -
79C LEU* 3.6 37.5 - - + -
80C CYS 2.9 11.1 + - - +
81C VAL* 3.5 8.6 - - + -
82C PHE* 3.0 34.7 + - - +
112C VAL* 4.0 5.4 - - + +
113C LEU* 1.3 77.9 - - - +
115C GLY* 1.3 59.8 + - - +
116C ASN 4.4 0.7 - - - +
142C ILE* 3.2 4.5 - - + +
144C THR* 3.3 40.4 - - + +
155C ALA* 3.9 13.5 - - + -
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Residues in contact with GLY 115 (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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82C PHE* 3.6 25.6 - - - -
84C ILE* 4.1 6.7 - - - -
114C VAL* 1.3 70.7 - - - +
116C ASN* 1.3 61.1 + - - -
118C CYS* 3.3 8.7 - - - -
141C TYR* 3.5 13.4 - - - -
142C ILE 2.9 10.7 + - - -
143C GLU* 3.4 0.9 - - - -
144C THR* 2.7 27.2 + - - -
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Residues in contact with ASN 116 (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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14C VAL 2.9 24.2 + - - +
15C GLY* 3.6 9.7 + - - -
19C LEU* 3.7 10.7 - - + +
81C VAL* 4.1 10.8 - - + -
82C PHE 2.8 18.8 + - - +
83C ALA* 3.5 1.2 - - - -
84C ILE* 2.9 23.0 + - - +
114C VAL* 3.7 0.4 + - + -
115C GLY* 1.3 73.4 - - - +
117C LYS* 1.3 81.4 + - - +
118C CYS 3.4 0.4 - - - -
144C THR* 2.8 23.1 + - - +
146C ALA* 3.3 18.9 + - - +
203C GNP 3.2 25.6 + - - -
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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