Contacts of the helix formed by residues 104 - 122 (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 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.4 23.7 - - + -
102B ARG 3.3 12.0 + - - +
103B GLU* 1.3 94.4 + - - +
105B PHE* 1.3 58.6 + - - +
107B GLU* 3.1 36.5 - - - +
108B LEU 2.9 23.9 + - - -
164B VAL* 3.7 15.9 - - + -
165B ASP* 5.2 6.8 + - - -
401B UDP 3.1 70.1 + - + +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.5 32.1 - + + -
103A GLU* 5.8 3.4 - - - +
105A PHE* 3.5 36.8 - + + -
108A LEU* 3.8 28.3 - - + -
130A VAL* 4.8 0.9 - - + -
132A ASN* 4.0 15.5 - - - -
300A LEU* 4.2 7.0 - - + -
309A VAL* 3.9 22.4 - - + -
101B PHE* 3.8 7.4 - - - -
103B GLU* 3.6 6.2 - - - +
104B ARG* 1.3 76.1 - - - +
106B GLU* 1.3 66.4 + - - +
108B LEU* 3.1 6.7 + - + +
109B LEU* 3.0 59.7 + - + +
300B LEU* 6.4 0.2 - - + -
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Residues in contact with GLU 106 (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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132A ASN* 4.6 6.7 - - - +
134A VAL* 3.6 41.3 - - + +
311A ASN* 4.3 13.2 + - - +
104B ARG 3.4 0.2 - - - -
105B PHE* 1.3 83.7 - - - +
107B GLU* 1.4 71.2 + - - +
109B LEU* 3.3 19.5 + - - +
110B VAL* 3.6 15.0 + - + +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 3.1 44.3 - - + +
106B GLU* 1.4 81.7 + - + +
108B LEU* 1.3 51.9 + - - +
110B VAL* 3.1 5.2 + - - +
111B PHE* 2.8 35.0 + - - +
164B VAL* 4.0 19.3 - - + +
165B ASP* 4.1 10.5 - - + -
258B LEU* 3.9 43.4 - - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.7 35.9 - - + -
99B VAL* 5.3 1.8 - - + -
101B PHE* 3.8 15.3 - - + -
104B ARG 2.9 13.6 + - - +
105B PHE* 3.4 12.8 - - + +
107B GLU* 1.3 76.1 - - - +
109B LEU* 1.3 65.8 + - + +
111B PHE* 4.1 4.7 - - + -
112B VAL* 3.0 52.1 + - + +
128B ILE* 5.9 0.2 - - + -
130B VAL* 3.9 22.4 - - + -
164B VAL* 3.8 18.6 - - + +
300B LEU* 4.1 15.3 - - + -
302B VAL* 4.7 2.9 - - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASN* 4.4 2.2 - - - +
298A THR* 4.1 21.1 - - + +
300A LEU* 3.9 28.0 - - + -
309A VAL* 3.8 18.8 - - + -
311A ASN* 4.1 18.4 - - - +
105B PHE* 3.0 53.6 + - + +
106B GLU* 3.6 8.3 - - - +
107B GLU 3.2 0.2 - - - -
108B LEU* 1.3 77.3 - - + +
110B VAL* 1.3 58.9 + - + +
113B PRO* 3.2 23.2 - - - +
302B VAL* 3.5 19.3 - - + +
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Residues in contact with VAL 110 (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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311A ASN* 6.1 2.5 - - - +
106B GLU* 3.6 12.5 + - + +
107B GLU 3.1 8.0 + - - +
109B LEU* 1.3 77.4 - - + +
111B PHE* 1.3 66.6 + - - +
113B PRO* 3.4 3.2 - - - +
114B HIS* 3.1 28.1 + - + +
167B LEU* 3.7 28.0 - - + -
256B ARG* 4.1 13.2 - - - +
258B LEU* 4.2 13.2 - - + -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 4.2 3.8 - - + -
99B VAL* 3.6 32.8 - - + -
107B GLU 2.8 16.7 + - - +
108B LEU* 3.1 5.8 + - + +
110B VAL* 1.3 78.6 - - - +
112B VAL* 1.3 69.3 + - + +
114B HIS* 3.2 0.7 + - - +
115B MET* 2.9 57.2 + - + +
128B ILE* 4.4 13.0 - - + -
162B HIS* 3.5 34.5 - + - -
163B ASP 3.5 8.3 - - - -
164B VAL* 3.3 35.4 - - + +
166B LEU 4.3 0.9 - - - -
167B LEU* 3.7 20.9 - - + -
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Residues in contact with VAL 112 (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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108B LEU* 3.0 41.0 + - + +
111B PHE* 1.3 83.8 - - + +
113B PRO* 1.4 70.2 - - + +
115B MET 3.5 0.2 + - - -
116B ARG* 3.0 23.6 + - - +
128B ILE* 4.0 12.7 - - + +
302B VAL* 3.9 12.1 - - + -
305B ALA* 3.3 29.2 - - + +
306B PRO 3.7 15.5 - - - +
307B CYS* 4.0 21.3 - - + -
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Residues in contact with PRO 113 (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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298A THR* 6.0 0.4 - - + -
84B TRP* 4.9 6.4 - - + -
109B LEU 3.2 25.6 - - - +
110B VAL 3.4 6.5 - - - +
112B VAL* 1.4 95.4 - - + +
114B HIS* 1.3 61.3 - - - +
116B ARG* 3.5 1.4 - - + +
117B ARG* 3.0 25.3 + - - +
302B VAL* 3.6 26.9 - - + +
303B GLY* 5.0 4.7 - - - +
305B ALA* 3.6 13.7 - - + -
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 3.1 26.4 + - + +
111B PHE* 3.5 6.1 - - - +
113B PRO* 1.3 78.4 - - - +
115B MET* 1.3 80.9 + - - +
117B ARG* 3.9 4.0 - - - +
118B PHE* 3.0 26.0 + + + +
167B LEU* 3.7 33.7 - - + +
168B PRO* 2.9 29.5 + - + +
169B LEU* 4.1 13.0 - - + -
256B ARG* 4.8 10.0 + - - -
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Residues in contact with MET 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 5.4 3.8 - - + -
111B PHE* 2.9 51.2 + - + +
114B HIS* 1.3 75.1 - - + +
116B ARG* 1.3 68.8 + - - +
118B PHE* 4.2 2.7 - - + -
119B LEU* 2.8 51.2 + - + +
126B HIS* 4.3 2.5 - - - -
128B ILE* 3.9 16.8 - - + -
162B HIS* 3.6 25.4 - - + +
168B PRO* 3.5 33.0 - - + -
175B TYR* 3.8 19.3 - - + -
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Residues in contact with ARG 116 (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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84B TRP* 3.5 43.0 + - + +
86B GLU* 5.1 6.1 + - - -
90B TRP* 5.9 2.2 - - - -
112B VAL 3.0 18.1 + - - +
113B PRO* 3.3 6.0 + - + +
115B MET* 1.3 77.6 - - - +
117B ARG* 1.3 56.6 + - - +
120B SER* 2.7 42.1 + - - -
126B HIS* 3.3 62.9 + - - +
127B HIS* 4.7 5.1 - - - +
128B ILE* 4.6 4.1 - - - +
305B ALA* 3.8 9.0 - - + -
306B PRO* 3.7 48.7 + - - +
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Residues in contact with ARG 117 (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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83B HIS* 3.9 20.4 + - + +
84B TRP* 4.1 13.6 - - + +
113B PRO 3.0 16.1 + - - +
114B HIS* 3.9 4.3 - - - +
116B ARG* 1.3 74.8 - - - +
118B PHE* 1.3 68.1 + - - +
120B SER* 3.3 0.3 + - - -
121B ARG* 2.9 54.0 + - + +
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Residues in contact with PHE 118 (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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114B HIS* 3.0 23.8 + + + +
115B MET* 3.8 6.7 - - + +
117B ARG* 1.3 86.6 - - - +
119B LEU* 1.3 73.3 + - + +
121B ARG* 3.5 4.7 + - - +
122B LYS* 3.2 49.6 + - + +
168B PRO* 3.7 41.3 - - + -
169B LEU 4.7 1.3 - - - -
170B ASN 3.6 29.6 - - - -
171B GLU* 3.9 12.3 - - + -
173B LEU* 4.5 1.3 - - + -
175B TYR* 3.6 33.7 - + - -
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Residues in contact with LEU 119 (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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95B LEU* 4.1 13.9 - - + -
97B VAL* 4.2 7.2 - - + -
115B MET* 2.8 42.8 + - + +
118B PHE* 1.3 79.7 - - + +
120B SER* 1.3 65.9 + - - +
122B LYS* 3.0 11.9 + - - -
124B ILE* 3.0 41.1 + - + +
126B HIS* 3.5 39.3 - - + +
175B TYR* 3.7 39.9 - - + -
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Residues in contact with SER 120 (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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83B HIS* 3.5 23.2 - - - +
84B TRP* 3.7 25.4 + - - +
90B TRP* 3.7 25.1 - - - -
116B ARG* 2.7 26.7 + - - -
117B ARG 3.8 2.0 - - - -
119B LEU* 1.3 77.5 - - - +
121B ARG* 1.3 59.3 + - - +
123B LYS* 2.9 21.1 + - - +
126B HIS* 3.9 9.4 - - - -
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B HIS* 3.6 34.6 - - + +
117B ARG* 2.9 41.5 + - + +
118B PHE* 4.0 4.5 - - - +
120B SER* 1.3 77.5 - - - +
122B LYS* 1.3 59.7 + - - +
123B LYS* 3.4 6.4 + - - +
171B GLU* 3.8 29.6 + - - +
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Residues in contact with LYS 122 (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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118B PHE* 3.2 48.1 + - + +
119B LEU* 3.0 8.4 + - - +
121B ARG* 1.3 77.6 - - - +
123B LYS* 1.3 70.6 + - - +
124B ILE* 3.2 17.2 + - + +
171B GLU* 2.7 43.8 + - + +
172B GLU* 4.5 1.0 - - - +
173B LEU 2.9 23.9 + - - -
174B ASP* 4.7 2.0 + - - +
175B TYR* 4.4 15.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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