Contacts of the strand formed by residues 173 - 179 (chain D) in PDB entry 1O1F
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 GLN 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D ALA* 3.6 24.5 - - + +
165D PHE* 3.6 9.3 + - - +
166D MET* 3.6 14.1 - - - +
169D ASP* 5.2 0.7 - - - +
171D GLU* 2.9 30.9 + - - +
172D ASN* 1.3 79.6 + - - +
174D SER* 1.3 58.4 + - - +
458D PHE* 3.2 7.8 + - - +
459D ILE* 3.6 23.6 - - + -
460D GLY* 3.0 20.6 + - - -
667D THR* 3.0 16.7 + - - +
668D HIS* 2.6 38.9 + - - +
670D HIS* 3.2 25.7 + - + -
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Residues in contact with SER 174 (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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173D GLN* 1.3 73.5 - - - +
175D ILE* 1.3 61.3 + - - +
176D LEU* 3.3 13.3 - - - +
249D PHE* 5.5 1.1 - - - -
460D GLY* 3.0 14.8 - - - -
462D LEU* 6.3 0.4 - - - -
490D PHE* 5.1 0.3 - - - -
664D LEU* 4.7 14.9 + - - +
667D THR* 2.9 27.7 - - - +
668D HIS 3.2 2.8 + - - -
669D PRO* 3.1 16.5 - - - +
670D HIS* 2.7 38.3 + - - +
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Residues in contact with ILE 175 (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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158D ILE* 4.0 21.3 - - + -
159D SER* 4.8 1.6 - - - -
162D ALA* 4.5 9.9 - - + -
174D SER* 1.3 79.7 - - - +
176D LEU* 1.3 64.9 + - - +
177D ILE* 3.5 26.5 - - + -
192D VAL* 4.7 10.5 - - + -
196D PHE* 4.2 18.6 - - + -
459D ILE* 4.2 22.7 - - + -
460D GLY 2.7 9.7 + - - +
461D VAL* 4.3 9.6 - - + +
462D LEU* 3.0 26.2 + - - +
670D HIS* 2.9 7.6 - - + +
672D VAL* 3.8 20.0 - - + -
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Residues in contact with LEU 176 (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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174D SER* 3.3 25.1 - - - +
175D ILE* 1.3 79.5 - - - +
177D ILE* 1.4 62.9 - - - +
178D THR* 5.9 0.7 - - - +
462D LEU* 3.6 32.8 - - + -
487D LEU* 4.6 10.3 - - + -
490D PHE* 4.5 10.5 - - + -
664D LEU* 4.4 16.6 - - + -
669D PRO* 4.5 2.9 - - + -
670D HIS 2.7 29.0 + - - +
671D PHE* 4.2 21.8 - - + -
672D VAL 2.8 25.9 + - - +
673D ARG* 3.0 17.2 + - - +
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Residues in contact with ILE 177 (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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155D ILE* 6.2 0.2 - - + -
175D ILE* 3.5 23.8 - - + -
176D LEU* 1.4 70.6 - - - +
178D THR* 1.3 70.0 + - - +
185D LYS* 3.6 22.1 - - + +
188D ASN* 4.8 4.0 - - + -
189D THR* 4.4 23.1 - - + +
192D VAL* 4.4 10.5 - - + -
461D VAL* 4.0 20.6 - - + -
462D LEU* 2.9 22.7 + - - +
463D ASP* 4.0 2.5 - - - -
464D ILE 3.7 12.6 + - - +
672D VAL* 3.4 24.7 - - + +
674D CYS* 3.5 27.8 - - - -
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Residues in contact with THR 178 (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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176D LEU* 5.4 0.3 - - - +
177D ILE* 1.3 81.5 + - - +
179D GLY* 1.4 61.3 + - - +
185D LYS* 4.3 3.8 - - - -
462D LEU* 5.7 3.1 - - - +
464D ILE* 3.5 16.7 + - - +
465D ALA 4.2 2.8 + - - -
466D GLY* 4.6 11.0 - - - -
484D ASN* 4.0 14.2 + - - +
487D LEU* 5.4 4.0 - - - +
672D VAL 3.3 4.9 + - - -
673D ARG* 3.6 39.7 + - - +
674D CYS* 2.9 26.2 + - - +
697D CYS 5.8 1.1 - - - +
698D ASN* 4.8 12.1 + - - +
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Residues in contact with GLY 179 (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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178D THR* 1.4 78.9 - - - +
180D GLU* 1.3 63.2 + - - -
183D ALA* 4.1 4.7 - - - -
185D LYS* 2.9 25.5 - - - +
464D ILE 4.3 1.0 + - - -
465D ALA* 4.2 1.4 - - - +
466D GLY* 3.8 17.9 + - - +
674D CYS* 3.7 15.3 - - - -
698D ASN* 5.4 3.8 - - - -
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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