Contacts of the strand formed by residues 25 - 33 (chain B) in PDB entry 1RHP
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 THR 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL 3.6 0.2 - - - +
30A ILE* 4.6 2.2 - - + -
31A LYS* 2.8 45.7 + - + +
23B HIS 3.6 1.2 + - - -
24B ILE* 1.3 69.7 - - - +
26B SER* 1.3 60.2 + - - +
44B THR 3.2 14.8 + - - -
45B LEU 3.8 7.8 + - - -
46B LYS* 4.1 14.2 - - + +
67B LEU* 3.1 14.2 - - - +
47C ASN* 3.2 25.0 + - - +
48C GLY* 4.1 6.7 - - - -
49C ARG* 4.1 28.7 - - - +
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLU* 3.2 27.4 + - - +
29A VAL 3.8 5.2 - - - -
30A ILE* 4.1 12.1 - - - +
24B ILE* 3.1 18.2 - - - +
25B THR* 1.3 77.7 + - - +
27B LEU* 1.3 63.1 + - - +
28B GLU* 5.6 1.7 - - - +
44B THR* 3.5 29.6 + - - -
48C GLY* 4.4 18.4 + - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU 4.0 0.3 - - - +
28A GLU* 3.6 1.8 - - - -
29A VAL* 2.9 35.4 + - + +
24B ILE* 4.2 4.7 - - + -
26B SER* 1.3 77.3 + - - +
28B GLU* 1.3 64.0 + - - +
29B VAL* 4.0 20.1 + - + -
41B LEU* 4.7 8.1 - - + -
42B ILE 3.6 10.8 - - - +
43B ALA* 4.5 0.4 - - + +
53B LEU* 3.9 18.2 - - + -
60B TYR* 5.4 0.4 - - + +
63B ILE* 3.5 38.6 - - + -
64B ILE* 4.0 24.0 - - + -
67B LEU* 3.4 20.6 - - + -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 3.5 13.6 + - - +
27A LEU 3.4 14.4 - - - +
28A GLU* 4.4 18.1 - - + +
26B SER* 5.6 2.7 - - - +
27B LEU* 1.3 74.2 - - - +
29B VAL* 1.3 62.5 + - - +
30B ILE* 3.4 31.7 + - + +
40B GLN 3.6 0.7 - - - +
41B LEU* 3.2 7.3 - - - +
42B ILE* 2.9 50.1 + - + +
50B LYS* 5.6 3.8 + - - -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 3.4 5.7 + - - -
27A LEU* 3.0 36.3 + - + +
29A VAL* 5.5 3.1 - - + -
64A ILE* 4.9 9.9 - - + +
67A LEU* 3.5 30.6 - - + +
68A LEU* 3.3 30.1 - - + -
27B LEU* 4.0 18.8 + - + +
28B GLU* 1.3 74.4 - - - +
30B ILE* 1.3 62.5 + - - +
39B ALA* 5.9 0.4 - - + -
40B GLN 3.8 3.4 - - - -
41B LEU* 3.6 18.8 - - + -
64B ILE* 4.5 11.4 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR 4.1 7.9 - - - +
26A SER* 4.5 5.8 - - - +
11B LEU* 4.3 12.8 - - + -
28B GLU* 3.4 29.2 - - + +
29B VAL* 1.3 79.8 - - - +
31B LYS* 1.3 69.8 + - - +
35B HIS* 4.2 9.0 - - + +
38B THR 4.3 0.4 - - - +
39B ALA* 3.1 8.8 - - - +
40B GLN* 3.0 54.1 + - + +
42B ILE* 3.3 31.2 - - + -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG 5.3 1.2 + - - -
24A ILE 4.4 7.0 + - - +
25A THR* 3.3 23.0 + - - +
46A LYS* 2.9 33.7 - - - +
66A LYS 3.9 9.2 - - - +
67A LEU* 3.4 48.4 - - + +
69A GLU 4.0 7.4 - - - +
70A SER* 3.8 23.6 - - - -
29B VAL 4.2 0.2 - - - -
30B ILE* 1.3 77.5 - - - +
32B ALA* 1.3 87.9 + - - +
35B HIS* 3.5 19.4 + - - -
38B THR 4.7 0.9 - - - -
39B ALA* 4.6 0.9 - - - +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 5.5 2.6 - - - +
69A GLU 4.2 7.1 + - - +
70A SER* 4.2 27.1 - - - +
30B ILE 4.0 0.6 + - - -
31B LYS* 1.3 100.0 - - - +
33B GLY* 1.3 60.1 - - - +
35B HIS* 4.4 2.3 - - - -
36B CYS 3.6 15.9 - - - +
37B PRO* 4.2 17.5 - - + +
38B THR 4.3 8.0 + - - +
39B ALA* 4.4 1.6 - - - +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA* 1.3 79.2 - - - +
34B PRO* 1.3 66.2 - - - +
35B HIS* 2.9 16.8 + - - -
36B CYS 3.3 12.2 + - - +
37B PRO* 4.3 3.9 - - - +
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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