Contacts of the strand formed by residues 119 - 134 (chain J) in PDB entry 2IVB
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 119 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG* 5.7 0.7 - - - -
124A ILE* 4.6 0.2 - - - -
93I THR* 2.7 28.8 + - - +
112J VAL* 4.7 1.0 - - - +
113J HIS* 3.5 7.2 - - - -
117J GLY 3.4 2.4 + - - +
118J ASP* 1.3 81.8 + - - +
120J ILE* 1.3 61.3 + - - -
150J TYR* 4.1 5.4 - - - -
151J LEU 3.3 12.6 - - - -
153J THR* 3.5 17.3 - - - -
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Residues in contact with ILE 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.7 30.1 - - + -
1161D AZI 3.3 33.7 - - - +
92I PRO* 3.9 9.0 - - + +
93I THR* 3.9 28.3 - - - +
96I ARG* 3.4 20.6 - - + +
112J VAL* 4.9 0.9 - - - -
119J GLY* 1.3 80.8 - - - +
121J ILE* 1.3 67.7 + - - +
122J ALA* 4.3 2.5 - - - -
150J TYR* 3.4 7.1 - - - -
151J LEU* 2.8 52.6 + - + +
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Residues in contact with ILE 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I THR* 5.0 4.0 + - + +
96I ARG* 3.3 25.2 - - - +
97I PHE* 4.6 10.3 - - + -
100I MET* 4.4 8.4 - - + +
142I ALA* 3.4 32.1 - - + -
144I ILE* 4.4 11.9 - - + -
112J VAL* 3.8 30.8 - - + +
116J PHE* 4.3 5.4 - - + -
120J ILE* 1.3 78.6 - - - +
122J ALA* 1.3 69.1 + - - +
126J PHE* 5.8 0.2 - - + -
148J GLY* 3.7 28.7 - - - +
149J LYS 3.5 0.9 - - - -
150J TYR* 3.9 27.6 - - + +
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Residues in contact with ALA 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 5.8 0.7 - - + -
1161D AZI 5.1 2.0 - - - +
100I MET* 3.8 3.8 - - - +
120J ILE* 3.9 10.5 - - + +
121J ILE* 1.3 73.0 - - - +
123J ALA* 1.3 59.2 + - - +
124J ILE* 3.4 12.6 - - + +
125J ASN* 4.0 22.2 - - + +
126J PHE* 3.5 18.5 - - - +
148J GLY* 3.7 8.7 - - - -
149J LYS* 2.8 20.1 + - + +
151J LEU* 4.0 20.9 - - + -
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Residues in contact with ALA 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ARG* 5.4 0.8 - - - +
96I ARG* 3.6 33.7 - - + +
99I GLU* 3.8 19.8 + - + +
100I MET* 3.7 22.9 - - + +
103I VAL* 5.6 6.6 - - + +
104I TYR* 5.2 5.0 - - - -
121J ILE 3.6 1.8 + - - -
122J ALA* 1.3 72.5 - - - +
124J ILE* 1.3 65.0 + - - +
126J PHE* 3.6 20.2 - - - +
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Residues in contact with ILE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLY* 4.5 1.3 - - - -
120A ILE* 3.5 42.0 - - + -
151A LEU* 3.8 16.6 - - + +
152A PRO 3.3 23.3 - - - +
153A THR* 3.0 42.1 + - - +
154A LYS 5.3 1.6 + - - +
92D PRO* 4.1 18.8 - - + -
96D ARG* 4.2 5.2 - - - +
1161D AZI 5.1 0.9 - - - +
99I GLU* 4.3 3.4 - - - +
103I VAL* 6.2 0.9 - - + -
81J ARG* 6.1 4.5 - - - +
122J ALA* 3.4 4.0 - - + -
123J ALA* 1.3 82.9 - - - +
125J ASN* 1.3 63.1 + - + +
126J PHE* 2.9 14.4 + - - +
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Residues in contact with ASN 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 6.6 0.7 - - + -
152A PRO 5.0 6.1 - - - +
135I ASP* 5.0 0.8 + - - -
137I GLU* 5.2 6.5 + - - +
141I ARG* 3.0 31.3 + - - +
122J ALA* 4.0 9.6 - - + +
124J ILE* 1.3 74.6 - - + +
126J PHE* 1.3 58.6 + - - +
127J LYS* 5.6 1.0 - - - +
148J GLY* 3.4 2.8 - - - -
149J LYS* 3.3 48.6 + - + +
151J LEU* 6.1 1.3 - - + -
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Residues in contact with PHE 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.8 17.2 - - - -
100I MET* 3.5 37.0 - - + -
104I TYR* 3.9 24.9 + + + -
144I ILE* 6.5 0.2 - - + -
121J ILE* 5.8 0.7 - - + -
122J ALA 3.5 15.5 - - - -
123J ALA* 3.6 26.0 - - - +
124J ILE 2.9 8.9 + - - +
125J ASN* 1.3 75.8 + - - +
127J LYS* 1.3 65.9 + - - +
128J LEU* 3.7 27.8 - - + -
146J LEU* 3.6 41.1 - - + -
147J ASP 3.4 18.8 - - - -
148J GLY* 4.0 1.1 - - - -
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Residues in contact with LYS 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.6 40.6 + - + +
141I ARG* 4.4 10.5 - - - +
125J ASN* 5.6 0.9 - - - +
126J PHE* 1.3 81.4 - - - +
128J LEU* 1.3 61.9 + - - +
129J ASP* 5.4 0.2 - - - +
145J THR 3.5 0.9 - - - +
146J LEU* 4.1 0.2 - - - -
147J ASP* 2.9 52.4 + - + +
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Residues in contact with LEU 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 3.7 12.2 - - + -
100I MET* 6.1 1.1 - - + -
104I TYR* 3.5 61.0 - - + -
107I THR* 5.9 0.2 - - + -
108I LEU* 4.7 19.7 - - + -
39J ALA* 5.7 0.3 - - - +
41J ALA* 3.6 24.2 - - + +
126J PHE* 3.7 21.1 - - + -
127J LYS* 1.3 74.8 - - - +
129J ASP* 1.3 69.3 + - - +
130J VAL* 6.0 1.6 - - + -
144J ILE* 5.3 1.6 - - + -
145J THR 3.1 13.0 - - - +
146J LEU* 4.3 13.5 - - + -
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Residues in contact with ASP 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J ALA* 5.1 0.2 - - - -
127J LYS 5.4 0.3 - - - +
128J LEU* 1.3 80.1 - - - +
130J VAL* 1.3 65.1 + - - +
131J LYS* 3.3 39.4 + - - +
143J VAL 3.7 1.4 - - - +
144J ILE* 3.4 4.7 - - - +
145J THR* 3.1 51.5 + - - +
1158J CL 3.4 14.1 - - + -
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Residues in contact with VAL 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I LEU* 3.9 28.0 - - + +
111I LEU* 4.3 19.5 - - + -
112I VAL* 4.5 11.9 - - + -
115I LYS* 3.4 34.0 + - + -
116I PHE* 4.1 24.5 - - + -
41J ALA* 6.2 0.2 - - + -
128J LEU* 6.0 2.0 - - + -
129J ASP* 1.3 77.6 - - - +
131J LYS* 1.3 68.1 + - - +
142J ALA* 4.8 0.2 - - + -
143J VAL 3.8 1.8 - - - -
144J ILE* 4.3 18.4 - - + +
1158J CL 3.0 16.0 - - + +
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Residues in contact with LYS 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I LYS* 5.5 0.4 - - - +
116I PHE* 3.9 4.0 - - - -
129J ASP* 3.3 26.2 + - + +
130J VAL* 1.3 76.3 - - - +
132J LYS* 1.3 64.5 - - - +
133J VAL* 3.9 7.1 + - + -
141J ARG 3.6 0.3 - - - +
142J ALA* 3.5 5.9 - - - +
143J VAL* 2.9 47.9 + - + +
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Residues in contact with LYS 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I LYS* 2.8 35.6 + - + +
116I PHE* 3.5 38.2 + - + +
130J VAL 4.4 0.2 + - - -
131J LYS* 1.3 73.6 - - - +
133J VAL* 1.3 71.0 + - - +
140J GLU* 2.9 42.5 + - + +
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Residues in contact with VAL 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J LYS* 4.7 9.2 - - + +
132J LYS* 1.3 83.1 - - - +
134J ALA* 1.3 73.8 + - - +
140J GLU* 3.4 2.7 - - - -
141J ARG* 2.5 51.6 + - + +
143J VAL* 4.5 20.4 - - + -
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Residues in contact with ALA 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J LYS* 5.1 0.4 - - - +
133J VAL* 1.3 89.0 - - - +
135J ASP* 1.3 64.2 + - - +
136J PRO* 3.8 6.2 - - - +
139J GLY 3.5 9.9 - - - +
140J GLU* 4.2 7.7 - - + +
141J ARG* 4.6 1.7 - - - +
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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