Contacts of the strand formed by residues 137 - 143 (chain D) in PDB entry 1FPY
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 ASP 137 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR 4.9 2.3 + - - +
167C GLY* 3.5 12.7 - - - -
168C ASN* 2.7 35.7 + - - +
135D PHE* 3.6 4.3 - - - +
136D ASP* 1.3 85.8 - - + +
138D ILE* 1.3 62.0 + - - +
139D ARG* 2.6 37.1 + - - +
150D ALA 4.6 1.4 - - - +
151D ILE* 3.7 1.9 - - - -
152D ASP* 2.9 48.2 + - + +
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Residues in contact with ILE 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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160C SER 4.0 1.9 - - - +
168C ASN* 2.9 37.0 + - - +
169C LYS 4.0 2.5 - - - -
170C GLY* 3.9 17.3 - - - +
135D PHE* 5.0 3.1 - - + -
137D ASP* 1.3 74.8 - - - +
139D ARG* 1.3 68.0 + - - +
140D PHE* 4.0 13.0 - - + -
149D VAL* 4.3 9.2 - - + -
150D ALA 3.4 16.2 - - - +
151D ILE* 4.0 21.8 - - + -
252D THR* 4.0 2.7 - - + +
462J PHE* 4.4 7.9 - - + -
466J TYR* 3.5 51.8 - - + +
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Residues in contact with ARG 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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160C SER 3.3 7.9 - - - +
161C SER 3.7 12.1 + - - +
162C THR 3.5 20.0 - - - +
163C LYS* 3.4 46.8 - - - +
168C ASN* 3.8 6.7 - - + +
137D ASP* 2.6 43.1 + - - +
138D ILE* 1.3 81.0 - - - +
140D PHE* 1.3 64.1 + - - +
148D HIS* 4.4 6.8 + - + +
149D VAL* 3.2 2.3 - - - +
150D ALA* 2.6 61.9 + - + +
152D ASP* 5.8 0.6 - - - +
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Residues in contact with PHE 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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160C SER* 3.0 61.3 + - - -
161C SER 3.1 2.8 + - - -
170C GLY* 4.8 15.3 - - - -
138D ILE* 4.0 22.2 - - + -
139D ARG* 1.3 80.8 - - - +
141D GLY* 1.3 64.2 + - - +
148D HIS* 3.0 27.0 + - - +
149D VAL* 3.9 5.2 - - + -
459J PRO 4.5 3.4 - - - +
462J PHE* 3.6 38.6 - - + -
463J GLU* 3.4 35.4 - - + -
466J TYR* 4.5 9.4 - + + -
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Residues in contact with GLY 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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160C SER* 4.4 4.5 - - - -
161C SER* 4.7 3.4 - - - -
140D PHE* 1.3 83.4 - - - +
142D ALA* 1.3 61.8 + - - -
147D SER* 3.0 4.6 - - - -
148D HIS* 2.8 43.8 + - - +
459J PRO* 4.3 3.9 + - - +
460J VAL* 6.5 0.2 - - - -
463J GLU* 4.7 4.5 - - - -
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Residues in contact with ALA 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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141D GLY* 1.3 75.4 - - - +
143D SER* 1.3 62.5 + - - +
146D GLY 3.5 5.4 - - - +
147D SER* 3.8 12.8 - - - -
452D ARG* 4.6 6.7 + - - +
456D THR* 4.8 6.1 - - + -
460J VAL* 4.1 19.5 - - + +
463J GLU* 4.0 18.7 + - - +
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Residues in contact with SER 143 (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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142D ALA* 1.3 78.1 - - - +
144D ILE* 1.3 69.3 + - - +
145D SER* 3.0 23.3 + - - -
146D GLY 2.7 20.2 + - - +
158J TRP* 6.1 0.2 - - - +
261J PHE* 5.5 7.0 - - - +
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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