Contacts of the strand formed by residues 7 - 18 (chain L) in PDB entry 2IAN
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 PHE 7 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14K LEU* 3.5 6.1 - - - +
15K ASN* 2.7 58.9 + - + +
16K PRO* 5.5 1.1 - - + -
70K LEU* 3.8 7.6 - - + +
74K THR* 3.5 32.5 - - + +
79K TYR* 3.8 15.5 - + + -
80K THR 3.2 45.5 - - - -
81K PRO* 3.6 11.7 - - + -
5L PRO* 4.4 15.9 - - + -
6L ARG* 1.3 76.2 - - - +
8L LEU* 1.3 59.8 - - - +
32L TYR* 3.4 10.1 - - - +
33L ASN* 3.7 4.5 - - - +
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Residues in contact with LEU 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K PHE* 3.8 20.6 - - + -
13K TYR 3.2 23.3 - - - +
14K LEU* 4.2 14.4 - - + -
70K LEU* 3.6 4.8 - - - +
82K ILE* 3.9 12.1 - - + -
113K THR* 3.7 23.6 - - - +
115K PRO* 3.9 15.5 - - + -
145K PHE* 4.0 5.6 - - + -
7L PHE* 1.3 75.5 - - - +
9L TRP* 1.3 68.8 + - - +
10L GLN* 3.9 23.3 - - + +
32L TYR* 3.4 9.9 - - - -
33L ASN* 2.9 41.3 + - - +
34L GLN 5.2 1.8 - - - +
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Residues in contact with TRP 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K PHE* 3.3 4.7 - - - +
13K TYR* 2.9 34.7 + - + +
66K ASP* 3.8 38.7 + - + +
69K ASN* 3.8 28.3 - - + +
70K LEU* 3.5 23.8 - - + -
73K MET* 3.8 44.4 - - + -
8L LEU* 1.3 75.3 - - - +
10L GLN* 1.3 76.5 + - - +
11L LEU* 4.7 5.6 - - + +
30L CYS* 3.6 36.3 - - + -
31L ILE 3.3 21.5 - - - -
32L TYR* 4.0 15.0 - + + -
37L SER* 4.3 9.0 - - - -
38L VAL* 5.1 2.9 - - + -
61L TRP* 5.3 0.2 - + - -
34M VAL* 4.6 5.4 - - + -
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Residues in contact with GLN 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K GLU 3.4 4.8 + - - +
12K PHE* 3.9 12.4 - - + +
143K HIS* 3.3 20.4 + - - +
144K LEU 5.0 0.2 + - - -
145K PHE* 3.2 32.4 - - - -
8L LEU* 3.9 17.7 - - + +
9L TRP* 1.3 85.2 - - - +
11L LEU* 1.3 60.5 + - - +
12L LYS* 3.8 24.4 - - - +
29L ARG 3.4 1.0 - - - +
30L CYS* 3.3 5.9 - - - +
31L ILE* 2.7 68.9 + - + +
34L GLN 4.5 2.8 + - - -
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Residues in contact with LEU 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K GLN 3.6 2.8 - - - +
10K ALA* 3.7 0.2 - - - -
11K GLU* 2.8 58.8 + - + +
62K ASN* 4.4 0.2 - - - +
66K ASP* 3.8 13.9 - - - +
69K ASN* 6.3 1.1 - - - +
9L TRP* 4.7 6.8 - - + +
10L GLN* 1.3 72.5 - - - +
12L LYS* 1.3 60.3 + - - +
13L PHE* 3.6 26.5 - - + -
28L GLU* 4.6 17.0 - - + +
29L ARG 3.3 6.1 - - - +
30L CYS* 3.7 28.7 - - - -
31M ALA* 3.7 33.4 - - + -
32M ALA 5.5 4.0 - - - +
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Residues in contact with LYS 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ILE* 4.4 10.3 - - + +
9K GLN 3.3 3.6 - - - +
10K ALA* 4.3 13.0 - - + -
11K GLU 5.1 0.9 - - - +
139K PRO* 3.4 28.5 - - + +
140K ARG 2.8 31.9 + - - +
143K HIS* 3.7 20.1 + - + +
10L GLN* 3.8 23.9 - - + +
11L LEU* 1.3 79.0 - - - +
13L PHE* 1.3 64.1 + - - +
14L GLU* 3.9 18.1 + - + +
27L LEU 3.8 1.0 - - - +
28L GLU* 3.4 4.3 - - - +
29L ARG* 2.8 42.9 + - + -
31L ILE* 4.2 15.5 - - + -
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Residues in contact with PHE 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE 3.5 2.4 - - - +
8K ILE* 3.2 4.0 - - - -
9K GLN* 2.7 62.0 + - + +
11K GLU* 4.6 0.7 - - - -
11L LEU* 3.6 28.9 - - + -
12L LYS* 1.3 73.1 - - - +
14L GLU* 1.3 61.4 + - - +
15L CYS* 3.9 0.3 + - - -
26L LEU* 4.0 4.7 - - + -
27L LEU 3.9 1.1 - - - -
28L GLU* 3.2 41.7 - - + -
71L ARG* 3.8 19.5 - - - -
78L TYR* 3.5 21.7 + - + +
29M LEU* 3.2 50.7 - - + -
30M ASN 4.0 1.8 - - - -
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Residues in contact with GLU 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 4.8 0.9 - - + -
7K ILE 3.5 4.3 - - - -
8K ILE* 3.8 33.0 - - + +
141K GLU* 4.5 10.1 - - - +
143K HIS* 5.6 0.2 - - - -
12L LYS* 4.6 15.7 - - + +
13L PHE* 1.3 74.1 - - - +
15L CYS* 1.3 60.8 + - - +
16L HIS* 2.8 32.4 + - + +
25L ARG 3.7 0.5 - - - +
26L LEU* 3.3 8.8 - - - +
27L LEU* 2.9 50.3 + - + +
29L ARG* 3.2 32.8 + - - +
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Residues in contact with CYS 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 3.4 4.0 - - - -
7K ILE* 2.7 44.7 + - + +
14L GLU* 1.3 74.5 - - - +
16L HIS* 1.3 62.1 + - - +
17L PHE* 3.3 24.0 - - + -
25L ARG 3.7 3.1 - - - -
26L LEU* 4.2 0.9 - - - -
78L TYR* 3.5 26.0 - - - -
79L CYS* 2.1 50.3 - - - -
82L ASN* 6.0 1.6 - - - -
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Residues in contact with HIS 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K GLU* 2.8 27.4 + - - +
5K HIS 3.8 2.9 - - - -
6K VAL* 3.6 18.3 - - + +
141K GLU* 5.9 2.5 - - - -
14L GLU* 2.8 44.4 + - + +
15L CYS* 1.3 74.0 - - - +
17L PHE* 1.3 59.6 + - - +
18L PHE* 4.2 10.4 - - + -
23L ARG 3.8 0.2 - - - +
24L VAL* 3.1 10.2 - - - +
25L ARG* 2.8 78.0 + - + +
27L LEU* 4.5 4.2 - - + +
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Residues in contact with PHE 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLU* 4.2 2.0 + - - +
4K GLU* 3.2 24.1 + - + +
5K HIS* 3.1 30.6 + - + +
7K ILE* 3.7 28.0 - - + -
15L CYS* 3.3 34.5 - - + -
16L HIS* 1.3 76.3 - - - +
18L PHE* 1.3 61.9 + - - +
19L ASN 4.2 0.2 - - - -
20L GLY 3.3 17.9 - - - +
21L THR* 4.5 1.8 - - + -
23L ARG 3.5 3.4 - - - +
24L VAL* 3.8 31.6 - - + -
79L CYS* 3.8 19.1 - - + -
80L ARG* 4.4 0.7 - - - -
83L TYR* 3.7 41.1 - + + -
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Residues in contact with PHE 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLU* 3.6 40.2 - - + +
4K GLU* 4.4 2.7 - - - +
16L HIS* 4.3 10.8 - + + -
17L PHE* 1.3 72.8 - - - +
19L ASN* 1.3 72.8 + - + +
20L GLY 3.8 0.2 - - - +
22L GLU 3.7 1.2 + - - -
23L ARG* 2.7 78.1 + - + +
25L ARG* 4.2 31.2 - - + -
43L ASP* 5.8 0.2 - - - -
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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