Contacts of the strand formed by residues 11 - 19 (chain A) in PDB entry 2IUK
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 ILE 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS* 1.3 68.6 - - - +
12A LYS* 1.3 61.5 + - - +
13A GLY 3.5 1.7 + - - -
70A LEU* 4.2 18.6 - - + -
110A PHE* 3.8 2.6 - - - -
111A PHE* 2.6 39.8 + - + +
112A GLU 4.1 7.0 - - - +
113A TRP* 3.6 40.4 - - + -
120A PRO* 4.2 4.5 - - + -
140A LEU* 3.8 26.7 - - + -
141A GLU 3.1 18.6 - - - +
142A ASP 3.7 11.2 - - - +
143A ILE* 3.9 23.6 - - + -
144A PRO* 4.9 0.2 - - + -
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Residues in contact with LYS 12 (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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10A LYS 3.3 4.6 + - - -
11A ILE* 1.3 72.5 - - - +
13A GLY* 1.3 55.4 + - - +
14A THR* 3.7 18.4 + - - -
94A LEU* 4.4 13.6 - - - +
108A SER* 4.0 19.6 - - - -
110A PHE* 3.7 33.2 - - + -
140A LEU* 3.6 1.2 - - - -
141A GLU* 2.6 67.5 + - + +
142A ASP* 3.4 23.9 - - - +
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Residues in contact with GLY 13 (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 ILE 3.5 1.0 + - - -
12A LYS* 1.3 75.8 + - - +
14A THR* 1.3 64.7 + - - -
108A SER* 3.1 10.4 - - - -
109A ILE* 2.9 53.4 + - - +
111A PHE* 4.8 0.9 - - - -
139A LYS 3.5 7.9 - - - -
140A LEU* 3.9 7.4 - - - -
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Residues in contact with THR 14 (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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12A LYS* 3.7 14.0 + - - -
13A GLY* 1.3 75.8 + - - -
15A VAL* 1.3 61.8 + - - +
16A VAL* 4.1 14.1 + - + +
94A LEU* 3.9 22.9 - - + -
98A PRO* 5.2 11.0 - - + -
106A ALA* 5.3 1.3 - - + -
107A PHE 3.3 3.6 - - - +
108A SER* 4.5 0.2 - - - +
109A ILE* 4.0 0.8 - - - +
138A VAL* 3.0 6.5 + - - +
139A LYS* 2.8 69.3 + - + +
141A GLU* 4.2 5.5 + - - +
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Residues in contact with VAL 15 (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 THR* 1.3 74.6 - - - +
16A VAL* 1.3 65.7 + - - +
17A LEU* 4.2 10.3 - - + -
66A ILE* 6.2 0.9 - - + -
68A MET* 3.7 18.6 - - - -
90A LEU* 3.9 12.6 - - + -
105A ASP 3.8 1.0 - - - +
106A ALA* 3.5 2.8 - - - -
107A PHE* 2.6 49.1 + - + +
109A ILE* 3.6 32.1 - - + -
125A ILE* 5.3 1.8 - - + -
135A LEU* 3.5 30.3 - - + -
137A SER 3.5 4.5 - - - +
138A VAL* 3.8 6.3 - - + -
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Residues in contact with VAL 16 (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 THR* 4.9 11.7 - - + +
15A VAL* 1.3 77.8 - - - +
17A LEU* 1.3 65.9 + - - +
98A PRO* 6.1 1.3 - - + -
100A LEU* 3.9 24.5 - - + -
104A GLN* 3.4 39.5 - - + +
105A ASP 3.5 4.0 - - - +
106A ALA* 4.8 2.9 - - + -
135A LEU* 3.8 3.3 - - - +
136A VAL* 2.9 29.5 + - + -
137A SER* 2.8 36.8 + - - +
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Residues in contact with LEU 17 (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 VAL* 5.0 7.2 - - + -
16A VAL* 1.3 77.8 - - - +
18A MET* 1.3 70.8 + - - +
19A PRO* 4.3 4.0 - - + -
61A PHE* 3.8 36.6 - - + -
66A ILE* 4.8 7.9 - - + -
90A LEU* 5.0 3.6 - - + -
104A GLN* 3.4 1.4 - - - -
105A ASP* 2.9 39.3 + - + +
107A PHE* 3.7 33.7 - - + -
133A PHE* 3.7 33.9 - - + -
134A PHE 3.2 11.9 - - - +
135A LEU* 4.3 4.0 - - + -
136A VAL* 3.9 2.2 - - - -
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Residues in contact with MET 18 (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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17A LEU* 1.3 84.5 - - - +
19A PRO* 1.3 72.2 - - + +
22A VAL* 3.8 13.0 - - + -
23A LEU* 3.9 11.4 - - + -
101A GLY 4.8 3.4 - - - +
102A ALA* 6.0 0.2 - - + -
103A ARG* 4.1 10.3 - - + +
104A GLN* 3.5 31.9 - - + +
133A PHE* 3.8 0.5 - - - +
134A PHE* 2.8 62.3 + - + +
136A VAL* 3.9 6.3 - - + -
272A LEU* 3.7 33.0 - - + -
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Residues in contact with PRO 19 (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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17A LEU* 4.3 3.1 - - + -
18A MET* 1.3 93.3 - - + +
20A LYS* 1.3 61.4 + - - +
21A ASN* 3.4 23.8 - - - +
22A VAL* 3.0 28.3 - - + +
23A LEU* 4.1 3.8 - - - +
57A THR* 5.7 4.5 - - + +
61A PHE* 3.4 37.0 - - + -
103A ARG 4.1 4.5 - - - +
105A ASP* 3.9 25.6 - - - +
132A GLU 5.2 0.2 - - - +
133A PHE* 4.7 2.7 - - + -
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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