Contacts of the strand formed by residues 23 - 28 (chain D) in PDB entry 1I8F
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 GLN 23 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 5.8 0.2 - - - -
22D LYS* 1.3 77.9 - - - +
24D VAL* 1.3 65.4 + - - +
35D ARG* 4.1 29.7 + - - +
36D GLY* 3.4 23.2 - - - +
37D ILE* 4.1 9.6 - - + +
51D ASP 5.5 2.8 + - - -
53D GLU* 4.4 9.9 + - - -
78D PRO* 3.7 4.3 - - - +
79D VAL* 3.0 47.5 + - + +
81D GLY 5.4 1.6 - - - +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 5.3 7.2 - - - -
22D LYS 4.5 3.1 - - - +
23D GLN* 1.3 76.7 - - - +
25D LEU* 1.3 62.4 + - - +
26D VAL* 3.9 11.6 - - + +
34D ILE 3.9 0.2 - - - +
35D ARG* 3.2 8.1 - - - +
36D GLY 2.7 41.1 + - - +
38D LEU* 4.3 13.5 - - + -
47D LEU* 5.6 0.2 - - + -
49D LEU* 3.9 22.2 - - + -
76D ILE* 3.0 33.7 - - + -
77D SER 3.5 15.3 - - - +
78D PRO* 3.7 6.7 - - + -
79D VAL* 3.8 5.6 - - - -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 1.3 72.5 - - - +
26D VAL* 1.3 65.2 + - - +
27D LYS* 4.8 2.2 - - + -
33D GLU* 3.8 28.0 - - + +
34D ILE 3.5 15.0 - - - +
35D ARG* 3.7 17.0 - - + -
75D PHE* 3.8 16.4 - - + +
76D ILE* 3.3 5.5 - - - +
77D SER* 2.8 44.7 + - - +
79D VAL* 3.8 10.5 - - + +
54E GLU* 4.0 6.1 - - - +
63E ARG* 3.5 48.2 - - - +
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Residues in contact with VAL 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D VAL* 3.9 19.1 - - + -
25D LEU* 1.3 81.5 - - - +
27D LYS* 1.3 67.3 + - - +
28D LEU* 3.8 22.9 - - + -
32D HIS 4.0 0.5 - - - +
34D ILE* 2.8 49.7 + - + +
47D LEU* 3.9 27.4 - - + -
49D LEU* 4.5 11.2 - - + -
68D VAL* 5.1 1.8 - - + -
73D VAL* 4.2 4.7 - - + -
75D PHE 3.4 11.9 - - - +
76D ILE* 3.8 14.4 - - + -
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.8 3.6 - - + -
26D VAL* 1.3 79.5 - - - +
28D LEU* 1.3 66.8 + - - +
31D SER 6.5 0.2 - - - -
32D HIS 3.2 10.5 - - - +
33D GLU* 3.6 24.7 + - + -
73D VAL* 3.9 0.3 - - - -
74D LEU* 2.8 37.0 + - + +
75D PHE* 3.2 34.6 + - + +
1004D GOL 2.7 31.3 + - - -
32E HIS* 4.3 17.2 - - + -
54E GLU* 2.4 40.6 + - - +
56E ILE* 3.5 9.9 - - - +
63E ARG* 4.7 0.7 - - - +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 4.2 34.8 - - + +
75C PHE* 4.7 2.0 - - + -
26D VAL* 3.8 10.1 - - + -
27D LYS* 1.3 82.5 - - - +
29D ARG* 1.3 73.0 + - - +
31D SER* 3.5 4.2 + - - -
32D HIS* 2.8 33.5 + - + +
34D ILE* 3.7 27.6 - - + -
68D VAL* 3.8 14.8 - - + -
69D ARG 5.9 0.2 - - - +
72D ASN* 3.3 12.1 - - + +
73D VAL* 3.7 29.2 - - + +
74D LEU* 3.6 13.7 - - - +
32E HIS* 4.8 0.5 + - - -
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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