Contacts of the strand formed by residues 110 - 115 (chain A) in PDB entry 2PMW
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 LYS 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A GLN* 4.1 2.0 - - - +
109A THR* 1.3 75.1 - - - +
111A ILE* 1.3 70.5 + - - +
112A LEU* 3.4 24.7 + - + +
124A VAL* 3.4 2.5 - - - -
125A LYS* 2.7 60.3 + - + +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 4.0 28.7 - - + +
98A LEU* 5.1 1.8 - - + -
99A GLN* 3.6 35.7 - - + +
110A LYS* 1.3 74.9 + - - +
112A LEU* 1.3 62.9 + - - +
113A HIS 4.1 10.5 - - - +
114A VAL* 4.1 23.3 - - + -
122A PHE* 4.0 9.2 - - + -
123A LEU 3.7 4.3 - - - +
124A VAL* 3.8 27.1 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR* 4.2 14.4 - - + +
110A LYS* 4.0 40.2 - - + +
111A ILE* 1.3 73.4 - - - +
113A HIS* 1.3 64.8 + - - +
123A LEU* 2.7 40.0 + - + +
125A LYS* 4.1 23.3 - - + +
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Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 3.3 3.2 + - - +
112A LEU* 1.3 85.3 + - + +
114A VAL* 1.3 84.2 + - - +
115A PHE* 3.7 25.5 - + - -
116A HIS* 6.0 0.2 - - - -
122A PHE* 3.2 5.5 - - - +
123A LEU* 2.8 37.9 + - + +
266B ILE* 3.9 35.1 - - + +
269B GLU* 2.9 33.1 + - - -
273B LYS* 4.8 5.4 - - - -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.9 26.7 - - + -
91A SER* 4.2 13.7 - - - -
92A GLU* 4.2 20.0 - - + +
95A ALA* 5.3 2.5 - - + -
111A ILE* 4.1 17.5 - - + -
113A HIS* 1.3 94.2 + - - +
115A PHE* 1.3 64.7 + - - +
116A HIS* 3.4 15.3 + - + +
121A GLY 3.6 11.7 - - - +
122A PHE* 4.0 5.4 - - + -
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.1 18.8 - - + -
88A LEU* 4.2 3.6 - - - +
91A SER* 4.7 1.9 + - - -
113A HIS* 3.7 18.6 - + - -
114A VAL* 1.3 76.0 - - - +
116A HIS* 1.3 63.4 + - - +
119A LEU* 2.9 34.4 - - + +
120A PRO* 4.0 4.0 - - - +
121A GLY* 2.8 23.8 + - - +
122A PHE* 3.6 35.2 - - - -
123A LEU* 4.0 11.4 - - + -
262B SER* 4.8 3.4 - - - -
265B LEU* 3.9 32.1 - - + -
266B ILE* 3.8 21.1 - - + -
269B GLU* 3.1 22.9 - - + +
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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