Contacts of the strand formed by residues 115 - 118 (chain H) in PDB entry 1FSK
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 115 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H PRO* 4.5 11.0 - - + -
114H THR* 1.3 73.4 - - - +
116H SER* 1.3 80.9 + - - +
134H CYS* 3.1 28.3 - - - -
135H PHE 3.0 7.0 - - - +
136H LEU* 4.7 5.8 - - + -
194H CYS* 4.5 7.4 - - + +
196H ALA* 4.0 20.4 - - + -
205H ILE* 3.6 29.2 - - + +
207H LYS* 3.7 43.0 + - + +
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H THR* 4.0 8.5 + - - +
115H VAL* 1.3 83.5 + - - +
117H ILE* 1.3 61.8 + - - +
118H PHE* 3.6 23.7 - - - -
134H CYS* 3.0 7.0 - - - -
135H PHE* 2.9 35.2 + - - +
137H ASN* 6.0 0.2 + - - -
207H LYS* 4.8 3.6 - - - +
142I THR* 3.4 22.1 + - - +
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Residues in contact with ILE 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H SER* 1.3 73.1 - - - +
118H PHE* 1.3 75.0 + - - +
119H PRO* 4.1 4.3 - - - +
132H VAL* 3.9 7.6 - - + -
133H VAL 3.5 10.3 - - - +
134H CYS* 4.1 5.8 - - - -
148H TRP* 3.6 26.7 - - + -
192H TYR 3.9 11.7 - - - +
193H THR 4.1 0.4 - - - -
194H CYS* 3.9 7.4 - - + +
207H LYS* 3.9 24.0 - - + +
208H SER* 3.8 29.8 - - - +
209H PHE* 3.9 23.6 - - + -
131I PRO* 5.5 1.2 - - - +
132I GLY 5.4 2.9 + - - -
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Residues in contact with PHE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H SER* 3.6 30.3 - - - -
117H ILE* 1.3 79.6 - - - +
119H PRO* 1.3 67.2 - - + +
131H SER 4.0 0.5 - - - +
132H VAL* 3.1 12.5 - - - +
133H VAL* 2.8 56.4 + - + -
135H PHE* 3.8 15.5 - + - -
209H PHE* 4.4 0.9 - - - -
129I LEU* 3.5 36.3 - - + -
130I ALA 3.2 30.3 - - - -
131I PRO* 3.9 6.7 - - + -
142I THR* 3.3 31.6 - - - -
143I LEU 4.2 5.2 - - - -
218I ARG* 4.6 1.8 - - - +
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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