Contacts of the strand formed by residues 115 - 119 (chain F) in PDB entry 4YHP
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 115 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A GLY* 3.4 28.9 + - - -
143E THR* 5.5 1.5 - - - +
191E THR* 6.1 0.2 - - - -
113F ALA 3.8 1.5 + - - -
114F PRO* 1.3 73.7 - - - +
116F VAL* 1.3 59.7 + - - +
117F PHE* 3.5 25.3 - - - -
136F LEU 3.3 2.8 - - - +
137F LEU* 3.5 1.6 - - - -
138F ASN* 2.7 46.3 + - - +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F PRO* 4.1 15.0 - - + +
115F SER* 1.3 76.8 - - - +
117F PHE* 1.3 76.2 + - - +
135F CYS* 3.8 15.5 - - - -
136F LEU 3.2 8.7 - - - +
137F LEU* 4.6 2.0 - - + -
195F CYS* 4.2 6.1 - - - -
197F VAL* 3.6 44.6 - - + -
202F LEU* 5.5 0.2 - - + -
206F VAL* 4.3 17.3 - - + -
208F LYS* 3.7 36.1 + - + +
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Residues in contact with PHE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E SER* 6.4 1.8 - - - -
143E THR* 4.0 26.2 - - + -
144E ALA* 4.2 2.7 - - - -
145E ALA* 3.5 44.9 - - + -
191E THR* 4.3 14.4 - - + -
115F SER* 3.5 35.9 - - - -
116F VAL* 1.3 79.6 - - - +
118F ILE* 1.3 61.3 + - - +
119F PHE* 4.1 8.5 - - + -
134F VAL 3.8 0.3 - - - +
135F CYS* 3.3 5.5 - - - -
136F LEU* 2.6 55.9 + - + -
138F ASN* 4.4 2.7 - - + -
208F LYS* 4.2 6.1 - - - -
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ALA 5.0 0.5 - - - +
135E SER* 5.4 9.5 - - - -
117F PHE* 1.3 75.5 - - - +
119F PHE* 1.3 74.5 + - - +
120F PRO* 4.1 4.4 - - + +
133F VAL* 4.3 4.7 - - + -
134F VAL 3.4 7.2 - - - +
149F TRP* 4.0 21.3 - - + -
193F TYR 3.8 11.0 - - - +
195F CYS* 4.1 6.7 - - - +
208F LYS* 3.6 40.5 - - + +
209F SER 4.0 16.8 - - - +
210F PHE* 3.7 33.7 - - + -
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Residues in contact with PHE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 3.7 50.4 - - + +
133E ALA 3.4 22.0 - - - -
134E PRO* 4.7 1.1 - - + -
145E ALA* 3.3 45.5 - - + -
146E LEU* 4.0 5.2 - - - -
189E VAL* 4.8 2.5 - - + -
117F PHE* 4.1 9.2 - + + -
118F ILE* 1.3 78.7 - - - +
120F PRO* 1.3 70.0 - - + +
132F SER 4.3 0.3 - - - +
133F VAL* 3.5 7.6 - - - +
134F VAL* 2.8 51.2 + - + +
136F LEU* 4.0 26.2 - - + -
210F PHE* 4.4 3.4 - - - -
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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