Contacts of the strand formed by residues 98 - 104 (chain D) in PDB entry 4FQX
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 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D PRO 3.8 3.9 + - - -
97D PRO* 1.3 73.5 - - - +
99D VAL* 1.3 61.5 + - - +
120D TRP* 3.0 68.6 + - - -
187D ARG* 5.9 0.7 - - - +
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Residues in contact with VAL 99 (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 PRO 3.6 14.1 + - - +
98D SER* 1.3 80.5 - - - +
100D GLN* 1.3 65.3 + - - +
117D CYS* 4.6 5.6 - - - -
118D TYR 3.2 11.9 - - - +
119D VAL* 4.1 11.4 - - + -
120D TRP* 4.0 0.4 - - - -
174D CYS* 4.9 0.9 - - + +
176D VAL* 3.9 31.2 - - + -
185D ILE* 4.0 20.9 - - + -
186D LEU 5.4 0.2 - - - -
187D ARG* 2.6 61.0 + - + +
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Residues in contact with GLN 100 (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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112C GLU* 5.3 6.6 - - - +
197C LEU* 3.5 32.2 - - + +
99D VAL* 1.3 80.9 + - - +
101D VAL* 1.3 70.0 + - - +
116D ALA 3.6 0.5 - - - +
117D CYS* 3.5 0.9 - - - -
118D TYR* 2.9 34.5 + - + +
120D TRP* 3.6 25.5 - - + -
187D ARG* 4.5 10.5 - - - +
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Residues in contact with VAL 101 (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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197C LEU* 5.4 0.4 - - - +
100D GLN* 1.3 82.8 - - - +
102D ALA* 1.3 63.8 + - - +
115D LEU* 4.1 24.0 - - + -
116D ALA 3.4 7.6 - - - +
117D CYS* 4.1 3.8 - - - -
131D TRP* 4.4 5.6 - - + -
174D CYS* 3.4 37.2 - - + +
187D ARG* 3.8 18.0 - - + +
188D ASP 4.7 10.0 - - - +
189D TRP* 4.3 27.2 - - + -
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Residues in contact with ALA 102 (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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195C ASN 5.9 0.2 - - - +
197C LEU* 3.9 20.6 - - + -
198C PRO* 3.8 28.5 - - + -
100D GLN 4.3 0.2 - - - -
101D VAL* 1.3 77.1 - - - +
103D LYS* 1.3 70.3 + - - +
115D LEU* 3.4 6.8 - - - -
116D ALA* 2.8 32.8 + - - +
118D TYR* 4.5 6.1 - - + -
189D TRP* 5.0 4.5 - - - +
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Residues in contact with LYS 103 (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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195C ASN* 4.8 8.5 - - - +
196C ALA 5.3 3.3 - - - +
198C PRO* 5.5 4.7 - - - +
102D ALA* 1.3 84.6 - - - +
104D THR* 1.3 62.7 + - - +
113D VAL* 3.9 25.9 - - + +
114D MET 3.4 8.1 - - - +
115D LEU* 4.1 4.9 - - + +
118D TYR* 4.9 1.4 + - - -
189D TRP* 3.8 37.6 - - + +
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Residues in contact with THR 104 (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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195C ASN* 3.0 36.5 + - - +
103D LYS* 1.3 77.9 - - - +
105D THR* 1.3 68.8 + - - +
106D PRO* 3.2 10.2 - - - +
107D PHE* 5.2 1.1 - - + -
114D MET* 2.9 40.1 + - + +
116D ALA* 3.9 25.1 - - + -
118D TYR* 4.3 4.1 + - - -
161D HIS* 3.9 12.1 - - + +
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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