Contacts of the strand formed by residues 22 - 30 (chain D) in PDB entry 1RGQ
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 SER 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A SER 4.1 4.9 - - - +
41A THR* 4.4 9.0 - - - -
42A ALA 5.2 0.9 + - - -
65A ARG* 4.3 4.9 + - - +
66A THR* 2.6 35.5 + - - -
67A ILE 3.9 5.4 + - - -
68A ALA* 4.4 15.8 - - - -
73A PRO* 4.3 8.6 - - - +
21D GLY* 1.3 73.6 - - - -
23D VAL* 1.3 63.4 + - - +
24D VAL* 3.8 9.5 + - - +
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Residues in contact with VAL 23 (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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39A VAL* 3.7 33.2 - - + -
40A SER 3.7 10.1 - - - +
41A THR* 4.1 5.2 - - + -
46A PHE* 4.5 5.8 - - + -
62A ALA* 4.0 9.9 - - + -
65A ARG* 3.8 25.6 - - + -
66A THR 2.7 19.5 + - - +
67A ILE* 3.4 14.4 - - + +
68A ALA 3.1 21.7 + - - +
88A TRP* 3.8 27.1 - - + -
22D SER* 1.3 71.8 - - - +
24D VAL* 1.3 61.9 + - - +
25D ILE* 5.3 0.5 - - - +
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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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39A VAL* 3.4 4.5 - - - +
40A SER* 2.9 49.8 + - - +
41A THR* 5.6 1.3 - - - +
68A ALA* 3.8 23.6 - - + -
22D SER* 3.8 8.9 + - - +
23D VAL* 1.3 75.7 - - - +
25D ILE* 1.3 64.2 + - - +
26D VAL* 3.9 10.4 + - + -
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Residues in contact with ILE 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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37A GLN* 4.0 17.0 - - + -
38A ILE 3.6 4.9 - - - +
39A VAL* 4.1 16.2 - - + -
67A ILE* 5.3 10.5 - - + -
68A ALA* 5.2 10.8 + - - +
91A PRO* 3.8 34.8 - - + -
92A GLN 5.7 1.3 - - - +
23D VAL 5.3 2.0 - - - +
24D VAL* 1.3 78.0 - - - +
26D VAL* 1.3 62.2 + - - +
27D GLY 3.4 25.6 - - - +
28D ARG* 4.6 6.5 - - + -
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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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38A ILE* 2.9 36.5 + - + +
40A SER* 4.1 29.6 - - - -
45A THR* 4.7 3.6 - - - +
112A ARG* 5.4 1.3 - - - +
41C LYS* 5.0 6.7 - - - +
24D VAL* 4.4 10.8 - - + -
25D ILE* 1.3 76.3 - - - +
27D GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 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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37A GLN* 3.9 0.5 - - - -
38A ILE* 3.0 37.3 + - - -
37C ILE* 5.3 3.6 - - - -
41C LYS* 5.8 3.1 - - - -
25D ILE* 3.4 11.1 - - - +
26D VAL* 1.3 78.2 - - - +
28D ARG* 1.3 69.9 + - - +
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Residues in contact with ARG 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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31A GLN 5.3 0.2 + - - -
32A VAL 3.3 25.1 + - - -
34A GLY* 4.8 3.1 - - - -
36A VAL 3.5 6.5 - - - +
37A GLN* 4.5 12.8 - - + +
38A ILE* 4.1 2.3 - - - +
92A GLN 5.2 2.5 - - - -
93A GLY* 3.6 30.3 + - - -
37C ILE* 3.2 11.5 - - - +
38C ILE* 3.0 73.3 + - + +
39C PRO 4.6 5.3 + - - -
41C LYS 5.7 2.8 + - - -
25D ILE* 4.6 9.6 - - + -
27D GLY* 1.3 80.5 - - - +
29D ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 29 (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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34A GLY* 3.6 1.6 - - - -
35A GLU* 3.3 22.2 + - - +
36A VAL* 2.8 38.8 + - + +
38A ILE* 4.1 15.0 - - + -
47A LEU* 5.3 1.3 - - + -
110A VAL* 4.4 17.9 - - + -
111A THR 3.5 23.8 - - - +
112A ARG* 3.8 21.1 - - - +
114A ALA* 4.3 8.7 - - + +
35C PRO* 4.7 2.7 - - + -
36C ALA 3.3 15.3 - - - +
37C ILE* 3.9 15.5 - - + -
38C ILE* 4.6 0.2 - - - -
28D ARG* 1.3 79.6 - - - +
30D VAL* 1.3 70.1 + - - +
31D LEU* 4.0 1.2 + - + -
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Residues in contact with VAL 30 (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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32A VAL* 3.8 11.4 - - + -
33A GLU 3.2 27.4 - - - +
35A GLU* 3.5 4.0 - - - +
35C PRO* 3.3 0.9 - - - +
36C ALA* 2.8 48.2 + - + +
38C ILE* 3.7 30.2 - - + +
29D ILE* 1.3 71.6 - - - +
31D LEU* 1.3 63.5 + - - +
32D SER* 4.4 9.4 - - - +
33D GLY* 3.6 9.7 + - - +
34D LYS* 4.0 25.8 - - + +
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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