Contacts of the strand formed by residues 114 - 118 (chain A) in PDB entry 1ANF
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ALA 3.9 1.1 + - - -
113A LEU* 1.3 71.4 + - - +
115A LEU* 1.3 64.6 - - - +
116A ILE* 3.7 2.8 + - - +
226A ILE* 3.4 7.1 - - - +
227A ASN 3.1 31.0 + - - +
232A TRP* 5.8 2.0 - - - -
244A VAL* 3.4 32.1 - - - +
245A THR 3.6 4.2 + - - -
247A LEU* 3.7 6.5 - - - -
319A ALA 3.9 6.2 + - - -
320A THR* 4.0 11.7 + - - -
323A ASN* 2.9 19.9 + - - +
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Residues in contact with LEU 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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114A SER* 1.3 72.9 - - - +
116A ILE* 1.3 59.6 + - - +
117A TYR* 5.0 2.2 - - + -
125A PRO* 4.0 19.3 - - + -
126A PRO* 4.3 11.7 - - + +
132A ILE* 6.1 1.1 - - + -
147A LEU* 4.7 4.0 - - + -
224A MET* 3.9 35.4 - - + -
225A THR 3.8 14.1 - - - +
226A ILE* 4.3 11.4 - - + -
244A VAL* 3.4 2.4 - - - -
245A THR* 2.7 57.0 + - + +
246A VAL 3.8 16.8 - - - +
247A LEU* 3.6 9.5 - - + +
248A PRO* 4.0 20.2 - - + -
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Residues in contact with ILE 116 (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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114A SER 4.1 8.1 - - - +
115A LEU* 1.3 74.6 - - - +
117A TYR* 1.3 64.0 + - - +
217A PHE* 3.6 22.7 - - + -
224A MET* 3.1 5.5 - - - +
225A THR* 2.9 42.0 + - + +
227A ASN* 3.9 37.5 - - + +
228A GLY 4.9 0.2 - - - +
231A ALA* 4.9 0.7 - - + -
232A TRP* 4.2 15.5 - - + +
235A ILE* 3.7 30.3 - - + -
242A TYR* 4.0 8.7 - - + -
243A GLY 3.2 11.0 - - - +
244A VAL* 4.3 14.1 - - + -
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Residues in contact with TYR 117 (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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115A LEU* 4.5 1.6 - - + -
116A ILE* 1.3 78.0 - - - +
118A ASN* 1.4 61.2 - - - +
119A LYS* 3.7 25.4 - - + -
122A LEU* 3.0 33.7 - - + -
123A PRO 3.5 14.2 + - - -
125A PRO* 3.7 35.0 - - + +
217A PHE* 3.7 5.2 - - - -
223A ALA 3.3 4.7 - - - +
224A MET* 3.7 19.1 - - + -
242A TYR* 3.0 6.9 - - - +
243A GLY* 2.7 59.6 + - - -
244A VAL 4.1 0.9 - - - -
245A THR* 3.8 25.0 - - + -
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Residues in contact with ASN 118 (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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117A TYR* 1.4 70.3 - - - +
119A LYS* 1.3 53.1 + - - +
120A ASP* 3.0 23.4 + - - +
121A LEU* 3.3 20.6 + - + +
122A LEU* 2.8 35.2 + - - +
217A PHE* 3.7 13.9 + - + -
220A GLY* 4.3 21.0 - - - -
222A THR 4.5 2.4 + - - +
223A ALA* 2.7 25.6 + - - +
240A VAL* 3.9 22.7 - - - +
241A ASN 3.6 6.6 + - - +
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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