Contacts of the strand formed by residues 127 - 131 (chain N) 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 VAL 127 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123M GLU* 4.7 1.2 - - - +
125N PRO* 5.0 0.9 - - + -
126N SER* 1.3 69.8 - - - +
128N PHE* 1.3 64.7 + - - +
129N PRO* 4.1 0.5 - - - +
146N CYS* 3.8 9.2 - - + -
147N LEU 3.3 9.4 - - - +
148N VAL* 4.8 2.9 - - + +
202N CYS* 3.7 31.0 - - + -
204N VAL* 3.6 26.0 - - + -
213N VAL* 3.4 32.4 - - + +
214N ASP 5.0 1.6 - - - +
215N LYS* 3.6 37.3 - - + +
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Residues in contact with PHE 128 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M PRO 5.1 1.6 - - - +
121M SER* 4.7 1.1 - - - +
124M GLN* 2.7 58.1 - - + -
129M THR* 5.4 7.0 - - - -
131M SER* 5.7 0.9 - - - -
126N SER* 3.1 41.3 - - - -
127N VAL* 1.3 79.8 - - - +
129N PRO* 1.4 58.3 - - + -
130N LEU* 2.3 23.7 + - - -
146N CYS* 4.2 0.9 - - - -
147N LEU* 2.9 45.8 + - + +
149N LYS* 3.5 31.6 - - + -
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Residues in contact with PRO 129 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M SER* 3.3 31.5 - - - +
122M ASP 4.5 0.2 - - - +
123M GLU* 3.2 41.1 - - - +
124M GLN* 4.0 1.1 - - - +
127N VAL 3.9 2.4 - - - +
128N PHE* 1.4 80.8 - - + -
130N LEU* 1.3 71.7 + - + +
131N ALA* 2.7 10.6 + - - +
132N PRO* 5.0 0.5 - - - +
215N LYS* 4.0 21.8 - - + -
217N VAL* 4.9 9.6 - - + -
218N GLU 5.8 1.1 - - - +
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Residues in contact with LEU 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N PHE 2.3 17.1 + - - -
129N PRO* 1.3 61.8 - - - +
131N ALA* 1.3 68.7 + - - +
132N PRO* 3.9 0.5 - - - +
144N LEU* 2.9 34.5 - - + -
145N GLY 2.8 28.7 - - - +
146N CYS* 3.0 35.5 - - - +
147N LEU 4.4 0.2 - - - +
160N TRP* 2.5 41.3 - - + -
215N LYS 5.8 0.2 - - - +
217N VAL* 3.0 47.6 - - + +
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Residues in contact with ALA 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118M PHE* 3.2 39.4 - - + -
119M PRO* 3.2 30.7 - - + +
120M PRO 5.5 0.9 - - - -
121M SER* 5.5 1.8 - - - -
133M VAL* 6.1 0.4 - - + -
129N PRO 2.7 9.6 + - - +
130N LEU* 1.3 75.0 - - - +
132N PRO* 1.3 70.9 - - + +
144N LEU* 4.0 2.9 - - - -
145N GLY 3.5 16.1 + - - +
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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