Contacts of the strand formed by residues 37 - 46 (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 PRO 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER* 5.7 0.7 + - - -
10B CYS* 4.7 3.1 - - - -
32B ALA* 4.2 14.3 - - + +
33B GLY 4.3 4.9 - - - +
34B PRO 6.2 0.2 - - - -
35B HIS 4.6 0.7 - - - -
36B CYS* 1.3 84.4 - - - +
38B THR* 1.3 66.2 + - - +
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Residues in contact with THR 38 (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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30B ILE 4.3 1.2 - - - +
31B LYS 4.7 0.3 - - - -
32B ALA* 4.3 7.1 - - - -
35B HIS* 5.5 0.2 + - - -
36B CYS* 2.9 24.7 + - - +
37B PRO* 1.3 86.4 + - - +
39B ALA* 1.3 86.7 + - - +
40B GLN* 3.3 16.8 + - + +
55B LEU* 5.0 6.3 - - + -
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Residues in contact with ALA 39 (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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67A LEU 3.9 19.5 - - - +
68A LEU* 4.5 7.2 - - + -
69A GLU 4.3 8.8 + - - +
29B VAL* 5.9 0.2 - - + -
30B ILE 3.1 14.4 - - - +
31B LYS* 4.7 0.2 - - - -
32B ALA* 4.4 5.9 - - - +
38B THR* 1.3 91.8 - - - +
40B GLN* 1.3 59.9 + - - +
41B LEU* 5.3 0.4 - - + -
55B LEU* 3.4 38.7 - - + +
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Residues in contact with GLN 40 (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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9B GLN 4.9 0.6 + - - -
10B CYS* 3.7 1.4 - - - -
11B LEU* 2.8 35.5 + - - +
12B CYS* 3.2 27.1 + - + +
28B GLU 3.6 0.9 - - - +
30B ILE* 3.0 50.8 + - + +
35B HIS* 3.8 17.2 + - - -
36B CYS* 3.7 29.8 - - - +
38B THR* 3.3 16.5 + - + +
39B ALA* 1.3 75.6 - - - +
41B LEU* 1.3 64.6 + - - +
42B ILE* 3.9 5.8 - - + -
55B LEU* 5.1 0.4 - - - -
11D LEU* 6.0 1.0 - - - +
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Residues in contact with LEU 41 (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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68A LEU* 3.7 14.8 - - + -
12B CYS* 5.0 2.0 - - - -
27B LEU* 4.7 8.5 - - + -
28B GLU 3.2 5.4 - - - +
29B VAL* 3.6 31.9 - - + -
39B ALA* 5.3 1.1 - - + -
40B GLN* 1.3 77.3 - - - +
42B ILE* 1.3 64.1 + - - +
52B CYS* 4.4 1.6 - - - -
53B LEU* 2.8 53.9 + - + +
54B ASP 4.5 5.2 - - - +
55B LEU* 3.5 31.6 - - + +
60B TYR* 3.5 37.9 - - + -
64B ILE* 5.4 1.6 - - + -
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Residues in contact with ILE 42 (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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11B LEU* 3.8 22.9 - - + -
12B CYS* 3.9 18.6 - - - -
27B LEU* 3.6 3.5 - - - +
28B GLU* 2.9 47.7 + - + +
30B ILE* 3.3 36.1 - - + -
40B GLN* 4.4 8.3 - - + -
41B LEU* 1.3 74.8 - - - +
43B ALA* 1.3 61.4 + - - +
44B THR* 4.3 2.9 - - - +
50B LYS* 4.2 34.3 - - + -
51B ILE 3.8 4.5 - - - -
52B CYS* 4.2 4.5 - - - +
8D LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 43 (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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24B ILE* 3.9 30.5 - - + -
26B SER 3.9 6.7 - - - -
27B LEU* 4.5 1.1 - - + +
42B ILE* 1.3 75.0 - - - +
44B THR* 1.3 60.4 + - - +
45B LEU* 3.5 2.1 + - + -
50B LYS* 3.4 2.7 - - - -
51B ILE* 2.7 50.2 + - + +
53B LEU* 4.1 14.8 - - + -
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Residues in contact with THR 44 (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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24B ILE* 3.9 0.6 - - - -
25B THR* 3.2 21.5 + - - -
26B SER* 3.5 24.8 + - - -
42B ILE* 4.3 2.6 - - - +
43B ALA* 1.3 68.4 - - - +
45B LEU* 1.3 69.4 + - - +
48B GLY 3.7 22.4 - - - +
50B LYS* 3.5 33.9 + - + +
46C LYS 4.1 15.5 - - - +
47C ASN 4.6 0.4 - - - -
48C GLY* 4.1 13.4 - - - +
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Residues in contact with LEU 45 (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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19B VAL* 3.5 31.9 - - + -
23B HIS* 3.6 17.5 - - + +
24B ILE* 3.6 19.1 - - + -
25B THR* 3.8 3.4 + - - -
43B ALA 3.5 1.7 + - - +
44B THR* 1.3 82.8 - - - +
46B LYS* 1.3 62.9 + - - +
47B ASN* 2.9 21.0 + - - +
48B GLY 3.6 7.4 + - - -
49B ARG 3.5 23.9 + - - +
51B ILE* 4.2 27.4 - - + -
47C ASN 4.7 1.4 - - - +
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Residues in contact with LYS 46 (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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31A LYS* 5.8 7.9 - - + +
22B ARG* 3.0 39.7 + - - +
23B HIS* 2.8 46.9 + - + +
24B ILE 5.0 4.0 - - - +
25B THR* 4.1 18.6 - - + +
45B LEU* 1.3 73.3 - - - +
47B ASN* 1.3 57.7 + - - +
47C ASN* 4.2 14.7 - - - +
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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