Contacts of the strand formed by residues 137 - 142 (chain D) in PDB entry 1FYT
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D GLN* 4.4 18.4 - - - -
128D LEU 5.0 3.6 - - - -
135D ASP 4.6 2.6 + - - -
136D LYS* 1.3 76.4 - - - +
138D VAL* 1.3 61.3 + - - +
139D CYS* 5.9 0.9 - - - -
181D TRP* 3.0 23.9 - - - +
182D SER 3.0 11.0 + - - -
183D ASN* 5.4 0.9 - - - -
184D LYS 5.3 3.8 + - - -
187D PHE* 4.0 19.9 + - - -
131E PHE* 4.9 0.9 - - - -
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLN* 3.6 3.6 - - - +
128D LEU* 3.1 43.7 + - + +
136D LYS* 4.7 0.4 - - + -
137D SER* 1.3 81.4 - - - +
139D CYS* 1.3 62.3 + - - +
179D VAL* 4.6 8.3 - - + -
180D ALA 3.3 7.9 - - - +
181D TRP* 3.7 5.8 - - + -
131E PHE* 3.5 43.4 - - + -
147E VAL* 4.6 7.9 - - + -
149E LEU* 3.4 33.2 - - + -
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Residues in contact with CYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D VAL* 4.2 2.0 - - + -
126D TYR 3.2 5.2 - - - +
127D GLN* 4.4 1.6 - - - -
128D LEU* 4.3 0.7 - - - -
137D SER* 5.4 0.4 - - - -
138D VAL* 1.3 78.0 - - - +
140D LEU* 1.3 61.3 + - - +
141D PHE 4.1 0.2 - - - -
178D ALA 4.0 0.5 - - - +
179D VAL* 3.6 7.5 - - - +
180D ALA 2.9 31.5 + - - +
187D PHE* 3.9 22.0 - - - -
189D CYS* 2.0 58.6 - - + -
192D ALA* 4.2 4.0 - - + -
193D PHE* 4.2 18.0 - - + -
147E VAL* 6.4 0.2 - - - -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ALA 3.3 2.3 - - - +
125D VAL* 3.2 5.5 - - - -
126D TYR* 2.6 44.4 + - + +
128D LEU* 3.9 21.1 - - + -
139D CYS* 1.3 73.3 - - - +
141D PHE* 1.3 57.7 + - - +
142D THR* 3.6 18.7 + - + -
177D SER* 4.0 24.5 - - - -
178D ALA 3.9 1.6 - - - +
179D VAL* 3.8 23.8 - - + -
137E GLU* 4.6 6.1 - - - +
145E THR* 3.3 39.7 - - + +
147E VAL* 4.4 3.4 - - + -
196E ARG* 4.3 10.1 - - + -
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Residues in contact with PHE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 4.3 0.4 - - + -
124D ALA 3.2 24.5 - - - -
125D VAL* 3.8 15.0 - - + +
139D CYS 4.1 1.2 + - - -
140D LEU* 1.3 71.6 - - - +
142D THR* 1.3 59.4 + - - +
144D PHE* 3.4 39.6 - + + -
148D THR* 4.0 8.7 - - + -
150D VAL* 4.0 22.2 - - + -
177D SER* 3.1 4.3 - - - -
178D ALA* 2.9 33.9 + - + +
193D PHE* 3.6 38.3 - + + -
197D ILE* 4.0 21.3 - - + -
198D ILE* 3.6 30.7 - - + -
201D ASP* 4.6 3.1 - - + -
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Residues in contact with THR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PRO* 3.5 0.3 - - - +
124D ALA 3.0 25.5 + - - +
126D TYR* 3.5 36.1 - - + -
140D LEU* 4.1 15.5 - - + -
141D PHE* 1.3 76.3 - - - +
143D ASP* 1.3 82.5 + - + +
144D PHE* 3.0 13.6 + - - -
175D SER* 4.3 2.8 + - - -
176D ASN 3.1 13.0 + - - -
177D SER* 4.0 10.0 - - - -
145E THR* 5.3 0.3 + - - -
198E ARG* 4.1 18.9 + - - +
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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