Contacts of the strand formed by residues 94 - 101 (chain B) in PDB entry 4IRP
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU* 2.8 42.2 + - - -
92B PRO 4.1 0.8 + - - +
93B HIS* 1.3 75.8 - - - +
95B LEU* 1.3 60.9 + - - +
125B ARG* 3.5 30.5 - - + +
126B HIS* 4.1 15.4 + - - +
127B HIS* 5.4 2.7 - - - -
155B SER* 3.5 41.1 + - - +
156B THR* 3.4 18.1 - - + -
157B ASP* 2.8 36.1 + - - +
158B TYR* 3.4 7.1 + - - -
403B ACT 4.9 4.6 + - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ARG* 1.3 72.9 - - - +
96B ALA* 1.3 60.6 - - - +
97B VAL* 3.8 22.9 - - + -
119B LEU* 4.1 17.0 - - + -
124B ILE* 4.0 16.2 - - + -
125B ARG 2.8 17.5 + - - +
126B HIS* 3.2 3.0 - - + +
127B HIS 3.0 26.0 + - - -
156B THR* 3.8 3.9 - - - +
158B TYR* 3.7 32.3 - - + +
159B ILE 3.4 9.6 - - - +
160B ALA* 3.4 35.9 - - + +
175B TYR* 4.4 17.3 - - + +
205B LEU* 4.7 1.3 - - + -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 1.3 71.0 - - - +
97B VAL* 1.3 64.1 + - - +
98B LEU* 3.4 8.3 + - + +
127B HIS 3.6 4.5 - - - -
129B TYR* 3.9 18.4 - - + -
152B SER* 3.9 10.8 - - - -
156B THR* 3.4 28.1 - - + +
158B TYR 3.0 12.3 + - - +
159B ILE* 3.2 9.8 - - + +
160B ALA 2.8 24.1 + - - -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.8 26.9 - - + -
96B ALA* 1.3 72.3 - - - +
98B LEU* 1.3 59.5 + - - +
99B VAL* 3.8 20.4 - - + +
111B PHE* 4.2 10.8 - - + -
115B MET* 5.4 2.9 - - + -
119B LEU* 4.2 16.2 - - + -
126B HIS* 4.4 3.6 - - + -
127B HIS 2.8 20.0 + - - +
128B ILE* 4.0 16.8 - - + -
129B TYR* 2.8 33.1 + - - +
160B ALA* 3.7 5.4 - - + +
162B HIS* 4.0 22.0 - - + -
175B TYR* 6.5 0.2 - - + -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.9 24.5 - - + +
97B VAL* 1.3 77.1 - - - +
99B VAL* 1.3 60.1 + - - +
100B PRO* 3.3 5.4 - - - +
129B TYR* 3.8 13.5 - - + -
131B LEU* 3.7 10.8 - - + -
145B ILE* 3.7 30.4 - - + +
148B GLY* 3.9 24.7 - - - +
149B PHE* 3.5 26.0 - - - +
159B ILE* 4.0 22.2 - - + -
160B ALA 2.7 17.0 + - - +
161B MET 3.8 1.1 - - - +
162B HIS 3.0 23.9 + - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 3.8 15.0 - - + +
98B LEU* 1.3 75.0 - - - +
100B PRO* 1.3 66.4 - - - +
101B PHE* 3.6 7.0 - - + +
108B LEU* 5.3 2.0 - - + -
111B PHE* 3.6 31.6 - - + -
128B ILE* 4.2 6.3 - - + -
129B TYR 2.7 18.8 + - - +
130B VAL* 3.6 7.2 - - + -
131B LEU* 2.7 33.4 + - - +
162B HIS 3.6 6.7 - - - +
164B VAL* 3.5 43.1 - - + -
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU 3.3 12.8 - - - +
99B VAL* 1.3 86.3 - - - +
101B PHE* 1.3 61.0 + - - +
131B LEU* 3.9 13.6 - - + +
139B PHE* 3.8 13.9 - - + -
141B ARG* 3.8 41.3 - - + +
144B LEU* 4.3 11.2 - - + -
145B ILE* 4.6 8.5 - - + -
162B HIS 3.5 14.4 - - - +
163B ASP* 4.9 1.1 - - - +
401B UDP 2.8 34.4 + - - +
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Residues in contact with PHE 101 (chain B).
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* 3.5 30.1 - + - -
99B VAL* 3.6 8.5 - - + +
100B PRO* 1.3 77.1 - - - +
102B ARG* 1.3 68.3 + - - +
103B GLU 4.0 5.4 - - - -
104B ARG* 3.4 52.9 - - + -
105B PHE* 3.8 4.7 - - - -
108B LEU* 3.8 26.9 - - + -
130B VAL* 3.6 21.3 - - + -
131B LEU 3.0 21.4 + - - +
132B ASN* 3.7 14.3 - - - -
133B GLN 3.3 14.4 + - - -
139B PHE* 3.4 8.3 - - - -
164B VAL* 4.3 14.8 - - + -
401B UDP 3.1 4.7 - - - -
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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