Contacts of the strand formed by residues 135 - 146 (chain A) in PDB entry 2IIJ
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 LEU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.6 4.9 - - - +
18A PHE* 2.7 45.6 + - + +
84A ILE* 5.5 1.1 - - + -
89A ALA* 3.2 32.3 - - + +
90A VAL* 4.3 10.5 - - + -
115A ASN* 3.5 36.6 - - + +
116A GLU* 3.6 8.1 - - - +
117A TYR* 4.2 3.1 - - + +
118A THR* 3.8 2.4 - - - +
130A PRO* 6.0 0.2 - - + -
131A ASP 3.0 13.0 + - - +
132A PHE* 3.3 37.3 - - + +
133A SER 3.2 2.8 - - - +
134A LYS* 1.3 79.9 - - - +
136A GLN* 1.3 54.3 + - - +
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO* 3.0 38.4 + - - +
16A SER* 3.3 25.4 - - - +
17A PRO* 3.9 1.4 - - + +
114A ASN 3.2 5.5 - - - +
115A ASN* 3.3 2.5 - - - -
116A GLU* 2.9 42.6 + - - +
117A TYR 4.9 1.6 - - - -
118A THR* 3.3 34.1 - - + +
123A ARG* 4.7 9.8 + - - +
134A LYS 3.7 0.2 + - - -
135A LEU* 1.3 73.9 - - - +
137A ARG* 1.3 60.8 + - - +
138A ASN* 3.4 3.0 + - - +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 2.6 32.2 + - - +
14A ASN 3.7 0.2 - - - -
15A PRO* 2.8 20.6 - - - +
16A SER 2.7 14.3 + - - +
17A PRO 4.1 0.9 - - - -
18A PHE* 2.7 53.9 + - + -
20A ASN* 2.6 32.7 + - - +
22A PHE* 3.1 49.4 - - - +
44A TYR* 4.4 1.6 - - - -
78A ALA* 3.6 11.7 - - - +
113A VAL* 3.6 8.3 - - + -
114A ASN 3.8 3.1 - - - -
115A ASN* 3.4 17.7 - - - +
136A GLN* 1.3 70.9 - - - +
138A ASN* 1.3 59.0 - - - +
139A ILE* 3.2 18.0 - - + +
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 4.5 0.5 + - - -
15A PRO* 3.2 37.5 - - + +
114A ASN* 2.8 53.7 + - + +
116A GLU* 6.1 1.8 - - + -
136A GLN* 3.4 3.2 + - - +
137A ARG* 1.3 69.3 - - - +
139A ILE* 1.3 64.6 + - - +
140A LEU* 3.0 37.3 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 3.8 21.1 - - + -
13A ASP* 3.1 44.6 - - - +
14A ASN* 2.8 22.3 + - - +
15A PRO 4.2 4.0 - - - -
22A PHE* 4.9 1.8 - - + -
24A PHE* 4.9 2.0 - - + -
95A VAL* 4.7 9.2 - - + -
111A TYR* 3.5 35.7 - - + -
112A TYR 3.5 4.5 - - - -
113A VAL* 4.0 13.7 - - + +
137A ARG* 3.2 32.9 + - + +
138A ASN* 1.3 71.9 + - - +
140A LEU* 1.3 49.8 + - - +
141A ALA 2.7 17.2 + - - -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 5.9 0.4 - - + -
111A TYR* 3.2 14.6 - - - -
112A TYR* 2.7 48.6 + - + +
114A ASN* 4.3 17.9 - - + +
138A ASN* 3.0 35.0 + - - +
139A ILE* 1.3 66.5 - - - +
141A ALA* 1.3 56.7 + - - +
142A SER* 3.0 20.9 - - - +
143A ASN* 3.0 28.7 + - + +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.5 8.1 - - + -
14A ASN* 4.3 15.0 - - - +
111A TYR* 3.2 23.0 + - + +
139A ILE 2.7 11.0 + - - +
140A LEU* 1.3 71.3 - - - +
142A SER* 1.3 58.1 + - - +
143A ASN 3.1 3.6 - - - -
144A PRO* 3.4 16.0 - - - +
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.0 20.6 - - - +
141A ALA* 1.3 80.2 - - - +
143A ASN* 1.3 63.0 + - - +
144A PRO* 3.5 4.6 - - - +
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Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLY 3.6 7.3 - - - +
112A TYR* 3.7 30.0 + - + -
140A LEU* 3.0 31.1 + - + +
142A SER* 1.3 86.3 + - - +
144A PRO* 1.3 62.8 - - - +
145A ARG* 3.4 9.2 + - - +
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Residues in contact with PRO 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.5 1.6 - - + -
109A VAL* 4.2 1.6 - - + -
110A GLY 4.0 4.5 - - - +
111A TYR* 3.6 38.1 - - + +
140A LEU 3.7 0.2 - - - -
141A ALA 3.4 17.9 - - - +
142A SER 3.5 3.4 - - - +
143A ASN* 1.3 84.9 - - - +
145A ARG* 1.3 61.5 + - - +
146A VAL* 3.0 25.7 + - + +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG 2.8 5.9 - - - +
110A GLY 2.8 42.6 + - - +
112A TYR* 5.2 5.8 - - + -
143A ASN* 3.4 6.7 + - - +
144A PRO* 1.3 68.5 - - - +
146A VAL* 1.3 65.6 + - - +
147A THR* 4.2 7.1 + - - +
127B ALA* 5.9 4.4 - - - +
130B ILE* 3.2 42.1 - - + +
131B ARG* 4.0 34.5 - - + +
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL 6.0 0.2 - - - +
107A ILE* 4.1 28.0 - - + -
108A ARG 3.2 6.1 - - - +
109A VAL* 4.1 13.2 - - + +
144A PRO* 3.0 28.7 + - + +
145A ARG* 1.3 80.2 + - - +
147A THR* 1.3 60.9 + - - +
148A ARG* 4.0 14.4 + - + +
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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