Contacts of the strand formed by residues 122 - 126 (chain A) in PDB entry 1F0K
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 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 4.7 6.3 - - + -
100A VAL* 3.7 20.6 - - + -
112A GLY* 3.7 28.0 - - - +
115A ALA* 3.9 1.3 - - + -
116A TRP* 4.2 9.4 - - + +
120A ILE 3.8 9.6 - - - +
121A PRO* 1.3 76.9 - - - +
123A VAL* 1.3 64.9 + - - +
124A LEU* 3.8 27.8 - - + -
138A LEU* 4.8 4.3 - - + -
141A ILE* 4.6 6.3 + - + +
142A ALA* 3.7 16.5 - - + +
143A THR* 2.8 33.3 + - - -
144A LYS 3.4 4.5 + - - -
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Residues in contact with VAL 123 (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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99A VAL* 3.7 23.1 - - + -
100A VAL 2.9 10.6 + - - +
101A LEU* 3.2 8.6 - - + +
102A GLY 2.7 32.2 + - - -
122A VAL* 1.3 77.8 - - - +
124A LEU* 1.3 60.4 + - - +
144A LYS* 3.4 12.3 - - + +
146A MET* 3.4 32.3 - - + -
349A GLU* 5.2 0.2 - - + -
350A VAL* 4.1 22.9 - - + +
353A VAL* 3.8 27.8 - - + -
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Residues in contact with LEU 124 (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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101A LEU* 4.3 2.5 - - - -
102A GLY* 3.3 11.4 - - - +
122A VAL* 3.8 10.5 - - + -
123A VAL* 1.3 81.0 - - - +
125A HIS* 1.3 62.7 + - - +
135A ASN* 3.9 22.7 - - + +
138A LEU* 3.5 37.7 - - + -
139A ALA* 3.5 39.0 - - + +
142A ALA* 3.8 13.5 - - + -
144A LYS 2.9 10.5 + - - +
145A VAL* 3.9 12.7 - - + -
146A MET* 3.0 32.1 + - - +
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Residues in contact with HIS 125 (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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22A PRO* 5.0 1.6 - - + -
101A LEU* 4.4 4.0 - - + -
102A GLY 2.8 8.3 + - - -
103A MET* 3.5 37.6 - - + -
124A LEU* 1.3 77.2 - - - +
126A GLU* 1.3 63.8 + - - +
127A GLN* 3.0 40.6 + - + -
135A ASN* 3.4 12.3 - - - +
146A MET* 3.3 8.0 + - + +
148A ALA 4.0 12.1 - - - -
159A VAL* 3.6 16.5 - - + +
160A GLY 3.1 23.7 + - - -
161A ASN* 3.2 22.0 + - - -
162A PRO* 4.6 4.8 - - + +
346A VAL* 3.8 23.5 - - + +
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Residues in contact with GLU 126 (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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19A HIS* 5.1 5.8 - - - -
103A MET 5.2 0.2 - - - -
104A GLY* 5.3 0.9 - - - -
125A HIS* 1.3 74.9 + - - +
127A GLN* 1.3 61.7 + - - +
128A ASN* 2.9 51.0 + - - +
130A ILE 3.7 1.4 - - - +
131A ALA* 3.7 12.6 - - - -
132A GLY* 3.0 29.5 + - - -
135A ASN* 2.8 27.4 - - - +
145A VAL* 6.0 0.2 - - + -
146A MET 2.9 12.5 + - - +
147A GLN* 3.3 3.9 - - + +
148A ALA* 2.8 28.2 + - - +
152A ALA* 4.1 7.2 - - + -
153A PHE* 3.9 16.8 - - + -
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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