Contacts of the strand formed by residues 94 - 101 (chain D) in PDB entry 4IRQ
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 ARG 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D GLU* 4.0 19.4 + - - -
92D PRO 4.1 8.7 - - - +
93D HIS* 1.3 73.8 - - - +
95D LEU* 1.3 58.9 + - - +
125D ARG* 3.5 25.8 - - + +
126D HIS 3.7 28.0 + - - +
127D HIS* 4.1 20.0 + - - +
129D TYR* 5.7 0.4 + - - -
153D SER* 4.9 4.4 + - - -
155D SER* 3.1 44.4 + - - +
156D THR* 3.4 10.1 - - + +
157D ASP* 2.7 39.8 + - - +
158D TYR* 3.3 8.4 + - - +
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Residues in contact with LEU 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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94D ARG* 1.3 69.4 - - - +
96D ALA* 1.3 61.0 - - - +
97D VAL* 3.9 22.7 - - + -
119D LEU* 3.9 26.9 - - + -
124D ILE* 4.1 2.7 - - + -
125D ARG 2.7 17.3 + - - +
126D HIS* 3.1 5.8 - - + +
127D HIS 3.0 25.1 + - - -
156D THR* 4.0 2.8 - - - +
158D TYR* 3.5 41.0 - - + +
159D ILE 3.6 8.1 - - - -
160D ALA* 3.5 39.3 - - + +
175D TYR* 4.4 10.1 - - + +
205D LEU* 5.0 0.2 - - + -
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Residues in contact with ALA 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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94D ARG 3.7 1.8 + - - -
95D LEU* 1.3 72.8 - - - +
97D VAL* 1.3 62.3 + - - +
98D LEU* 3.5 8.0 + - + +
127D HIS 3.7 4.7 - - - -
129D TYR* 4.0 7.2 - - + -
152D SER* 3.8 21.8 - - - -
156D THR* 3.5 26.7 - - + +
158D TYR 2.8 13.3 + - - +
159D ILE* 3.3 9.8 - - + +
160D ALA 3.0 22.5 + - - -
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Residues in contact with VAL 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 LEU* 3.9 19.1 - - + +
96D ALA* 1.3 70.5 - - - +
98D LEU* 1.3 61.9 + - - +
99D VAL* 3.7 12.8 + - + +
111D PHE* 4.1 11.9 - - + -
115D MET* 5.4 3.4 - - + -
119D LEU* 3.8 29.2 - - + -
126D HIS* 4.6 2.2 - - + -
127D HIS 2.9 16.8 + - - +
128D ILE* 4.1 14.4 - - + -
129D TYR* 2.8 32.1 + - - +
160D ALA* 3.7 5.6 - - + +
162D HIS* 3.8 29.4 - - + -
175D TYR* 6.3 0.2 - - + -
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Residues in contact with LEU 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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96D ALA* 3.8 17.3 - - + +
97D VAL* 1.3 75.5 - - - +
99D VAL* 1.3 61.3 + - - +
100D PRO* 3.3 7.3 - - - +
129D TYR* 4.0 16.4 - - + -
131D LEU* 4.0 9.2 - - + -
145D ILE* 3.7 23.4 - - + +
148D GLY* 4.0 10.1 - - - -
149D PHE* 3.6 21.3 - - - +
152D SER* 3.4 20.9 - - - +
159D ILE* 3.8 33.7 - - + -
160D ALA 2.8 14.9 + - - +
161D MET* 4.5 0.2 - - - -
162D HIS* 2.9 22.8 + - - -
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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 VAL* 4.1 6.3 - - + -
98D LEU* 1.3 74.7 - - - +
100D PRO* 1.3 66.8 - - - +
101D PHE* 3.4 7.2 + - + +
108D LEU* 5.4 1.3 - - + -
111D PHE* 3.4 33.2 - - + -
128D ILE* 4.0 12.3 - - + -
129D TYR 3.0 16.8 + - - +
130D VAL* 4.4 6.5 - - + -
131D LEU* 2.7 34.1 + - - +
162D HIS 3.4 11.9 - - - +
164D VAL* 3.6 35.4 - - + -
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Residues in contact with PRO 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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98D LEU 3.3 11.2 - - - +
99D VAL* 1.3 86.5 - - - +
101D PHE* 1.3 58.6 + - - +
131D LEU* 4.1 9.9 - - + +
139D PHE* 3.9 13.2 - - + -
141D ARG* 3.8 48.7 - - + +
144D LEU* 4.2 5.8 - - + -
145D ILE* 3.9 10.2 - - + -
162D HIS 3.3 15.5 - - - +
163D ASP* 4.2 2.2 - - - +
402D UDP 2.8 37.3 + - - +
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Residues in contact with PHE 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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105A PHE* 3.7 25.6 - + + -
99D VAL* 3.7 10.1 - - + +
100D PRO* 1.3 75.6 - - - +
102D ARG* 1.3 64.2 + - - +
103D GLU 4.2 6.3 - - - -
104D ARG* 3.5 46.7 - - + -
105D PHE* 3.9 4.7 - - - -
108D LEU* 3.8 27.8 - - + -
130D VAL* 3.5 22.2 - - + -
131D LEU 3.0 14.0 + - - +
132D ASN* 3.2 28.7 - - - -
133D GLN 2.9 27.9 + - - -
139D PHE* 3.6 9.4 - - - -
164D VAL* 4.3 17.0 - - + -
402D UDP 3.2 5.2 - - - -
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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