Contacts of the strand formed by residues 18 - 25 (chain H) in PDB entry 2IPU
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 18 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H PRO* 3.4 38.4 - - + -
12H LEU* 3.6 9.0 - - + +
16H GLN 4.0 0.8 + - - -
17H THR* 1.3 70.9 - - - +
19H SER* 1.3 61.0 + - - +
20H LEU* 4.0 18.6 - - + -
80H LEU 3.6 1.2 - - - +
81H ARG* 3.3 6.9 - - - +
82H ILE* 2.8 73.5 + - + +
86H ASP* 5.3 1.1 - - + +
90H TYR* 3.9 29.8 - - + +
109H VAL* 3.6 26.2 - - + -
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Residues in contact with SER 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H SER 4.2 0.2 - - - +
8H GLY* 4.1 13.7 - - - -
9H PRO* 4.1 6.5 - - - +
17H THR* 3.8 9.7 + - - +
18H LEU* 1.3 76.2 + - - +
20H LEU* 1.3 62.2 + - - +
21H THR* 4.2 2.2 + - - -
80H LEU 3.6 3.8 - - - -
81H ARG* 3.7 17.3 - - - +
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H SER 3.5 6.7 - - - +
8H GLY* 4.1 4.7 - - - -
18H LEU* 4.0 16.8 - - + -
19H SER* 1.3 73.4 - - - +
21H THR* 1.3 64.1 + - - +
36H TRP* 3.8 19.5 - - + -
79H PHE* 3.3 8.3 - - - +
80H LEU* 2.8 53.2 + - + +
82H ILE* 4.9 0.4 - - + -
90H TYR* 3.3 38.1 - - + -
107H THR* 3.5 31.2 - - + -
109H VAL* 4.0 17.7 - - + -
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Residues in contact with THR 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H LYS 3.8 0.2 - - - +
6H GLU* 3.3 3.6 - - - -
7H SER* 2.7 53.0 + - - +
19H SER 4.8 2.3 + - - -
20H LEU* 1.3 77.0 + - - +
22H CYS* 1.3 64.2 - - - +
23H SER* 4.1 7.6 - - - +
36H TRP* 3.5 5.4 - - - -
77H GLN* 3.6 27.4 - - - +
78H VAL 3.5 3.4 - - - +
79H PHE* 3.7 23.1 - - + -
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Residues in contact with CYS 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.0 17.3 - - - -
5H LYS 3.5 6.7 - - - -
21H THR* 1.3 74.8 - - - +
23H SER* 1.3 62.1 + - - +
24H PHE* 4.1 9.6 - - - -
35H VAL* 4.4 0.2 - - - -
36H TRP* 3.5 14.6 - - + -
76H ASN 3.8 0.2 - - - +
77H GLN* 3.1 7.3 - - - +
78H VAL* 2.7 41.0 + - + +
92H CYS* 2.0 51.8 - - + -
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Residues in contact with SER 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H THR* 4.7 0.3 - - - +
4H LEU* 3.6 0.5 - - - -
5H LYS* 2.8 48.2 + - - +
7H SER* 5.6 0.7 + - - -
21H THR* 4.1 4.9 - - - +
22H CYS* 1.3 73.5 - - - +
24H PHE* 1.3 60.3 + - - +
75H ARG 5.7 0.4 - - - -
76H ASN 3.4 8.1 - - - -
77H GLN* 3.2 26.6 + - - -
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Residues in contact with PHE 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H THR 3.1 14.1 - - - +
4H LEU* 4.0 8.1 - - + -
22H CYS* 4.1 15.0 - - - -
23H SER* 1.3 77.1 - - - +
25H SER* 1.3 63.7 + - - +
27H PHE* 3.5 49.1 - + + -
29H LEU* 4.0 28.7 - - + -
35H VAL* 4.2 7.4 - + - -
73H ALA* 5.7 0.4 - - - -
76H ASN* 3.1 71.3 + - + +
77H GLN 3.9 5.2 - - - -
78H VAL* 3.9 21.3 - - + -
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Residues in contact with SER 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLN 4.0 3.3 + - - -
2H VAL* 3.3 2.9 - - - -
3H THR* 2.9 45.7 + - - +
24H PHE* 1.3 77.1 - - - +
26H GLY* 1.3 60.2 + - - +
27H PHE* 3.3 13.4 + - - +
76H ASN* 5.5 1.6 - - - -
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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