Contacts of the strand formed by residues 91 - 98 (chain D) in PDB entry 5FHK
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 GLY 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D SER* 1.3 81.0 - - - +
92D LYS* 1.3 61.8 + - - -
119D GLU 3.7 5.7 + - - -
120D ILE* 3.5 5.7 - - - +
121D ASN* 2.9 30.0 + - - +
277D LYS* 3.9 7.4 - - - -
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Residues in contact with LYS 92 (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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91D GLY* 1.3 73.4 - - - -
93D ILE* 1.3 71.6 + - - +
94D LYS* 4.6 13.9 - - + +
121D ASN* 3.3 8.7 - - + +
123D GLU* 3.1 20.3 + - + +
139D ASP* 4.1 4.7 - - - +
277D LYS* 2.8 27.0 + - - +
212E ARG* 3.0 46.6 - - - +
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Residues in contact with ILE 93 (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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92D LYS* 1.3 79.8 - - - +
94D LYS* 1.3 61.8 - - - +
95D ILE* 3.6 22.8 + - + -
113D PHE* 4.3 4.9 - - + -
120D ILE* 3.6 22.7 - - + -
121D ASN 2.8 11.5 + - - +
122D ILE* 3.6 8.8 - - + +
123D GLU 3.0 24.1 + - - +
139D ASP* 3.4 15.5 - - + -
140D VAL* 4.9 0.9 - - + -
277D LYS* 3.3 43.7 - - + +
278D VAL* 4.1 7.0 - - + +
281D PHE* 3.9 24.9 - - + -
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Residues in contact with LYS 94 (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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92D LYS* 4.3 14.8 - - + +
93D ILE* 1.3 70.9 - - - +
95D ILE* 1.3 61.1 + - - +
123D GLU* 3.6 34.5 + - + +
125D THR* 4.7 5.1 + - - -
137D GLU* 3.5 24.0 - - - +
138D TRP* 3.8 30.3 - - + -
139D ASP* 2.8 48.1 + - - +
140D VAL 3.3 5.2 + - - +
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Residues in contact with ILE 95 (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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93D ILE* 3.6 23.6 - - + +
94D LYS* 1.3 81.5 - - - +
96D SER* 1.3 62.1 + - - +
97D THR* 4.5 2.0 - - + -
110D LEU* 4.0 22.2 - - + -
122D ILE* 3.6 22.9 - - + -
123D GLU 2.9 15.1 + - - +
124D LEU* 3.5 26.2 - - + -
125D THR 2.9 25.1 + - - -
138D TRP* 3.5 8.8 - - - -
140D VAL* 3.2 24.7 - - + +
142D PHE* 4.6 7.0 - - + -
281D PHE* 4.2 11.0 - - + -
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Residues in contact with SER 96 (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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95D ILE* 1.3 73.4 - - - +
97D THR* 1.3 63.5 + - - +
125D THR 3.3 5.4 - - - -
127D GLU* 3.4 29.1 - - - +
130D ALA* 5.4 0.7 - - - +
133D LEU* 3.5 24.9 - - - +
138D TRP* 3.8 17.2 - - - -
140D VAL 3.0 6.1 + - - -
141D ILE* 3.6 8.4 - - - +
142D PHE* 2.7 35.1 + - - +
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Residues in contact with THR 97 (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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95D ILE* 4.5 2.5 - - + -
96D SER* 1.3 80.6 + - - +
98D PRO* 1.3 70.0 - - - +
102D THR* 2.6 31.5 + - + +
106D MET* 4.5 11.4 - - + -
110D LEU* 4.8 2.9 - - + -
124D LEU* 3.5 27.6 - - + +
125D THR 3.1 4.0 + - - -
126D THR* 3.1 9.9 - - - +
127D GLU* 2.8 26.8 + - - +
142D PHE* 3.6 23.3 - - + -
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Residues in contact with PRO 98 (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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97D THR* 1.3 87.7 - - - +
99D TYR* 1.3 69.9 + - - +
100D ASN 3.6 0.2 + - - -
101D LEU* 4.3 4.7 - - + -
102D THR* 2.8 31.1 + - - +
105D MET* 4.3 24.0 - - + -
106D MET* 5.1 2.0 - - + -
126D THR* 4.6 0.2 - - - -
127D GLU 3.5 6.7 - - - +
142D PHE* 3.1 27.8 - - + +
143D ARG* 4.8 1.8 - - - -
144D VAL* 3.7 32.1 - - + +
264D ILE* 5.0 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