Contacts of the strand formed by residues 119 - 134 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E THR* 2.7 29.8 + - - +
112G VAL* 4.7 1.1 - - - +
113G HIS* 3.5 7.1 - - - -
117G GLY 3.6 1.2 + - - -
118G ASP* 1.3 84.2 + - - +
120G ILE* 1.3 59.7 + - - +
150G TYR* 4.2 4.0 - - - -
151G LEU 3.3 11.7 - - - -
153G THR* 3.4 18.6 - - - -
81H ARG* 5.4 1.2 + - - -
124H ILE* 5.4 0.4 - - - -
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Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E PRO* 3.9 17.5 - - + +
93E THR* 3.8 27.1 - - - +
96E ARG* 3.4 36.6 - - + +
1158E AZI 3.4 22.2 - - - +
112G VAL* 4.9 1.1 - - - -
119G GLY* 1.3 80.2 - - - +
121G ILE* 1.3 66.3 + - - +
122G ALA* 4.3 1.1 - - - +
149G LYS 3.7 0.2 - - - +
150G TYR* 3.4 7.3 - - - -
151G LEU* 2.9 57.1 + - + +
124H ILE* 4.0 20.4 - - + -
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Residues in contact with ILE 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E THR* 4.9 4.4 + - + +
96E ARG* 3.1 28.1 - - - +
97E PHE* 4.7 12.7 - - + -
100E MET* 4.3 8.9 - - + +
142E ALA* 3.7 26.7 - - + -
144E ILE* 4.8 7.4 - - + -
112G VAL* 3.5 40.2 - - + +
116G PHE* 4.2 4.5 - - + -
120G ILE* 1.3 79.2 - - - +
122G ALA* 1.3 63.9 + - - +
126G PHE* 5.6 0.4 - - + -
148G GLY* 3.6 32.1 - - - +
149G LYS 3.5 1.6 - - - -
150G TYR* 4.0 21.5 - - + -
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Residues in contact with ALA 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E MET* 4.4 0.9 - - - +
1158E AZI 3.2 22.9 - - - +
120G ILE* 3.8 3.4 - - - -
121G ILE* 1.3 75.8 - - - +
123G ALA* 1.3 57.0 + - - +
124G ILE* 3.5 0.9 - - + -
125G ASN* 3.8 21.3 - - + +
126G PHE* 3.6 8.6 - - - +
148G GLY* 3.6 20.8 - - - -
149G LYS 2.9 17.6 + - - +
151G LEU* 3.8 22.0 - - + -
151H LEU* 5.7 0.9 - - + -
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Residues in contact with ALA 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ARG* 3.5 29.1 - - + +
99E GLU* 4.0 19.1 - - + +
100E MET* 3.5 23.1 - - + +
103E VAL* 5.7 5.5 - - + +
104E TYR* 4.8 6.9 - - - -
1158E AZI 3.4 5.5 + - - -
121G ILE 3.8 1.2 + - - -
122G ALA* 1.3 71.2 - - - +
124G ILE* 1.3 62.4 + - - +
126G PHE* 3.4 24.4 - - - +
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Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PRO* 4.2 16.4 - - + -
96C ARG* 4.3 4.5 - - - +
99E GLU* 4.5 1.1 - - - +
1158E AZI 4.1 13.0 - - - +
81G ARG* 5.8 5.4 - - - +
122G ALA* 5.2 0.4 - - + -
123G ALA* 1.3 80.5 - - - +
125G ASN* 1.3 60.6 + - + +
126G PHE* 3.0 12.6 + - - +
119H GLY* 4.5 1.3 - - - -
120H ILE* 3.7 38.6 - - + -
151H LEU* 3.8 14.1 - - + +
152H PRO 3.3 25.1 - - - +
153H THR* 3.0 38.8 + - + +
154H LYS 5.5 0.5 + - - -
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Residues in contact with ASN 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ASP* 4.9 1.0 + - - -
141E ARG* 2.9 26.6 + - - +
122G ALA* 3.8 12.3 - - + +
124G ILE* 1.3 77.4 - - + +
126G PHE* 1.3 57.7 + - - +
148G GLY* 3.3 1.6 - - - -
149G LYS* 2.9 55.7 + - + +
151G LEU* 6.0 2.0 - - + +
151H LEU* 6.1 4.5 - - + -
152H PRO 5.2 5.6 - - - +
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Residues in contact with PHE 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E MET* 3.5 37.7 - - + -
104E TYR* 3.9 26.5 + + - -
141E ARG* 4.0 2.4 - - - +
121G ILE* 5.9 0.2 - - + -
122G ALA 3.6 14.6 - - - +
123G ALA* 3.4 33.4 - - - +
124G ILE 3.0 8.0 + - - +
125G ASN* 1.3 78.1 + - - +
127G LYS* 1.3 79.3 + - - +
128G LEU* 3.8 13.2 - - + -
146G LEU* 4.0 20.0 - - + -
147G ASP 3.2 31.2 - - - -
148G GLY* 4.1 1.3 - - - -
156H PHE* 4.3 14.2 - - - -
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Residues in contact with LYS 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ARG* 4.6 2.2 - - - +
126G PHE* 1.3 84.2 - - - +
128G LEU* 1.3 70.7 + - - +
129G ASP* 3.8 27.3 + - - +
145G THR 3.9 0.9 - - - +
146G LEU* 3.9 0.5 - - - -
147G ASP* 3.0 53.1 + - + +
156H PHE* 3.7 33.4 - - + -
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Residues in contact with LEU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E TYR* 3.8 36.6 - - + -
107E THR* 4.8 5.6 - - + -
108E LEU* 3.7 38.6 - - + -
111E LEU* 5.7 1.1 - - + -
41G ALA* 4.0 28.1 - - + +
126G PHE* 3.8 17.3 - - + -
127G LYS* 1.3 82.9 - - - +
129G ASP* 1.3 68.1 + - - +
130G VAL* 4.9 2.9 - - + -
144G ILE* 3.8 21.8 - - + -
145G THR 3.4 4.0 - - - -
146G LEU* 3.8 13.2 - - + -
156H PHE* 4.3 6.5 - - + -
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Residues in contact with ASP 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G LYS* 3.8 24.6 + - - +
128G LEU* 1.3 78.7 - - - +
130G VAL* 1.3 64.4 + - - +
131G LYS* 3.2 35.3 - - - +
143G VAL 3.6 0.5 - - - +
144G ILE* 3.3 5.9 - - - +
145G THR* 2.9 55.8 + - - +
1159G CL 3.5 15.3 - - + -
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Residues in contact with VAL 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E LEU* 3.7 30.3 - - + -
111E LEU* 5.0 11.0 - - + -
112E VAL* 4.8 15.3 - - + +
115E LYS* 3.4 41.0 + - + -
116E PHE* 4.1 18.2 - - + -
128G LEU* 4.8 4.5 - - + -
129G ASP* 1.3 82.2 - - - +
131G LYS* 1.3 66.3 + - - +
142G ALA* 5.5 0.9 - - + -
143G VAL 3.7 3.8 - - - +
144G ILE* 4.2 13.7 - - + -
1159G CL 3.1 14.6 - - + +
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Residues in contact with LYS 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E LYS* 5.3 0.4 - - - +
116E PHE* 4.0 3.9 - - - -
129G ASP* 3.2 30.7 - - - +
130G VAL* 1.3 76.9 - - - +
132G LYS* 1.3 64.8 + - - +
133G VAL* 4.6 6.1 - - + -
142G ALA* 3.5 4.7 - - - -
143G VAL* 2.9 44.8 + - + +
145G THR* 5.8 1.1 - - - +
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Residues in contact with LYS 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E LYS* 2.7 36.2 + - + +
116E PHE* 3.5 28.6 + - + +
131G LYS* 1.3 74.5 - - - +
133G VAL* 1.3 70.7 + - - +
134G ALA 5.0 1.1 - - - +
140G GLU* 3.4 41.7 + - + -
141G ARG 3.6 4.3 - - - +
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LYS* 4.4 8.7 - - + +
132G LYS* 1.3 84.2 - - - +
134G ALA* 1.3 69.2 + - - +
136G PRO* 6.3 0.2 - - + -
140G GLU* 4.7 0.2 - - - -
141G ARG* 2.6 50.3 + - + +
143G VAL* 3.9 25.6 - - + -
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Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G LYS* 5.0 2.2 - - - +
133G VAL* 1.3 81.9 - - - +
135G ASP* 1.3 66.9 + - - +
136G PRO* 3.3 8.4 - - + +
139G GLY 3.6 9.4 - - - +
140G GLU* 4.4 6.3 - - + +
141G ARG* 4.4 0.6 - - - +
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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
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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