Contacts of the strand formed by residues 126 - 130 (chain L) in PDB entry 3KYM
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 SER 126 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126K LYS* 5.9 0.7 - - - -
127K SER* 5.7 0.5 + - - -
123L LYS* 5.1 8.7 + - - -
124L GLY 3.9 1.8 + - - -
125L PRO* 1.3 76.0 - - - +
127L VAL* 1.3 62.7 + - - +
128L PHE* 3.7 31.1 + - - -
147L LEU 3.8 0.5 - - - +
148L VAL* 3.7 2.8 - - - -
149L LYS* 3.0 35.4 + - - +
150L ASP* 4.7 4.0 + - - +
213L VAL* 6.3 0.2 - - - -
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Residues in contact with VAL 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K LYS* 5.2 0.7 + - - -
125L PRO 4.3 2.2 + - - +
126L SER* 1.3 77.5 - - - +
128L PHE* 1.3 67.9 + - - +
146L CYS* 4.2 4.3 - - + -
147L LEU 3.4 8.3 - - - +
148L VAL* 4.6 5.4 - - + -
202L CYS* 4.0 27.8 - - + -
204L VAL* 3.6 36.3 - - + -
213L VAL* 3.8 27.6 - - + +
214L ASP 5.6 0.2 - - - -
215L LYS* 3.2 38.3 + - + +
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Residues in contact with PHE 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K ASP* 5.4 4.0 - - - +
123K GLU 5.7 0.4 - - - -
124K GLN* 3.4 48.7 - - + +
126K LYS* 3.5 40.4 - - - -
127K SER* 4.8 5.2 - - - -
129K THR* 5.4 2.0 - - - -
126L SER* 3.7 32.5 - - - -
127L VAL* 1.3 81.6 - - - +
129L PRO* 1.3 72.0 - - + +
130L LEU* 6.1 0.7 - - + -
146L CYS* 3.4 5.2 - - - +
147L LEU* 2.8 58.2 + - + +
149L LYS* 4.7 13.0 - - + -
150L ASP* 5.8 0.9 - - - -
215L LYS* 5.2 0.7 - - - -
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Residues in contact with PRO 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D GLU* 4.3 15.0 - - + +
120K PRO* 5.3 1.7 - - - +
121K SER 6.0 0.2 - - - -
122K ASP* 3.0 44.7 - - - +
127L VAL 4.2 3.8 - - - +
128L PHE* 1.3 90.6 - - + +
130L LEU* 1.3 65.7 + - - +
131L ALA* 3.6 4.5 + - + +
145L GLY 4.0 5.6 - - - +
146L CYS* 4.7 0.9 - - - -
215L LYS* 4.3 22.2 - - + +
216L THR 4.9 1.8 - - - +
217L VAL* 3.7 29.8 - - + -
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Residues in contact with LEU 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120K PRO* 3.7 35.4 - - + -
131K SER* 6.3 0.9 - - - -
133K VAL* 3.9 19.5 - - + -
128L PHE* 3.7 0.9 + - + -
129L PRO* 1.3 73.7 - - - +
131L ALA* 1.3 59.5 + - - +
132L PRO* 4.8 0.2 - - - -
144L LEU* 3.4 8.8 - - - +
145L GLY* 2.9 44.4 + - - +
146L CYS 3.8 22.7 - - - +
147L LEU* 3.8 25.8 - - + +
185L SER* 3.8 22.0 - - - +
186L SER 4.6 0.4 - - - +
187L VAL* 4.6 6.5 - - + -
217L VAL* 4.2 2.0 - - - +
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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