Contacts of the strand formed by residues 45 - 54 (chain D) in PDB entry 5VXZ
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 GLY 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D ILE* 4.4 15.5 - - - -
43D LEU* 4.1 2.8 + - - +
44D THR* 1.3 75.2 + - - +
46D THR* 1.3 67.9 + - - +
96D ARG* 3.7 4.1 - - - +
97D ILE* 2.9 34.6 + - - +
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Residues in contact with THR 46 (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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454B GLU* 6.3 0.4 - - + -
37D ILE* 3.7 8.7 - - - +
45D GLY* 1.3 80.8 - - - +
47D LEU* 1.3 72.6 + - - +
48D ARG* 6.0 0.5 - - - +
94D GLN* 3.9 27.9 + - + +
95D LEU* 3.2 13.2 - - - +
96D ARG* 3.7 37.2 - - - +
97D ILE* 6.1 0.4 - - - -
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Residues in contact with LEU 47 (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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34D PRO* 4.6 3.6 - - + -
35D GLY* 3.3 38.1 - - - +
36D ASN 4.6 0.9 - - - +
37D ILE* 3.8 20.9 - - + +
46D THR* 1.3 82.5 - - - +
48D ARG* 1.3 62.4 + - - +
62D TRP* 3.8 16.3 - - + -
94D GLN* 3.3 6.1 - - - +
95D LEU* 2.9 40.0 + - + +
97D ILE* 4.8 1.8 - - + -
108D TYR* 3.9 31.0 - - + -
124D GLY 5.7 0.2 - - - +
126D VAL* 3.9 24.2 - - + -
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Residues in contact with ARG 48 (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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455B ASP* 4.5 2.6 + - - -
456B THR* 5.9 0.8 + - - +
457B THR* 2.8 32.5 + - - +
460B GLU* 4.5 15.3 + - - -
32D SER* 4.4 10.8 + - - +
33D ASN 3.5 3.8 - - - +
34D PRO* 3.2 23.6 - - - +
35D GLY 4.4 1.9 + - - +
46D THR* 6.0 0.4 - - - +
47D LEU* 1.3 79.8 - - - +
49D CYS* 1.3 62.2 + - - +
50D GLN* 3.1 37.9 + - - +
62D TRP* 3.8 6.3 - - - -
92D ALA* 3.6 10.8 - - - +
93D SER 3.2 15.4 + - - +
94D GLN* 4.1 22.3 - - + +
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Residues in contact with CYS 49 (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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30D PHE* 4.2 10.8 - - + -
32D SER* 3.2 16.4 - - - +
34D PRO* 4.2 8.3 - - + -
48D ARG* 1.3 77.9 - - - +
50D GLN* 1.3 62.3 + - - +
51D LEU* 4.9 3.1 - - - -
60D VAL* 4.0 14.8 - - - -
92D ALA* 3.3 4.7 - - - +
93D SER* 3.1 33.2 + - - +
110D CYS* 2.2 51.8 - - + -
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Residues in contact with GLN 50 (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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457B THR* 3.7 13.0 - - - +
460B GLU* 4.7 5.7 - - - +
461B THR* 5.1 1.2 + - - -
30D PHE* 3.5 4.4 - - - -
31D VAL* 2.8 37.3 + - + +
32D SER* 3.0 28.0 + - - +
48D ARG* 3.1 35.8 + - - +
49D CYS* 1.3 72.4 - - - +
51D LEU* 1.3 68.7 + - - +
90D ILE* 3.6 32.1 - - - +
91D VAL 3.1 13.5 - - - +
92D ALA* 3.9 2.2 - - + -
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Residues in contact with LEU 51 (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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29D PRO* 3.2 28.0 - - + +
30D PHE* 3.8 21.5 - - + -
31D VAL* 3.9 4.7 - - - +
49D CYS* 4.9 3.1 - - - -
50D GLN* 1.3 83.2 + - - +
52D GLN* 1.3 62.0 + - - +
53D VAL* 4.1 17.5 - - + -
58D PRO* 4.5 3.6 - - + -
60D VAL* 4.5 11.4 - - + -
89D TRP 3.6 0.2 - - - +
90D ILE* 3.6 5.5 - - - +
91D VAL* 2.8 58.7 + - + +
92D ALA* 5.2 0.2 - - - -
112D VAL* 3.8 34.1 - - + -
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Residues in contact with GLN 52 (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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29D PRO* 3.1 21.8 + - - +
31D VAL* 4.4 17.9 - - + +
51D LEU* 1.3 72.9 - - - +
53D VAL* 1.3 69.3 + - - +
81D LEU* 3.7 19.8 - - + +
88D ASP* 3.5 30.5 + - - +
89D TRP 3.0 20.4 - - - +
90D ILE* 4.4 11.8 - - + +
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Residues in contact with VAL 53 (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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29D PRO* 4.3 7.9 - - + -
51D LEU* 4.1 27.6 - - + -
52D GLN* 1.3 82.1 - - - +
54D GLN* 1.3 62.8 + - - +
55D GLY 3.9 17.3 - - - +
56D GLU 4.1 11.7 - - - +
57D PRO* 4.1 11.2 - - + -
58D PRO* 4.4 10.5 - - + -
88D ASP* 3.1 7.6 - - - +
89D TRP* 2.7 43.1 + - + +
91D VAL* 4.8 2.7 - - + -
114D LEU* 4.5 15.3 - - + -
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Residues in contact with GLN 54 (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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53D VAL* 1.3 77.5 - - - +
55D GLY* 1.3 66.7 + - - +
56D GLU 3.9 1.6 + - - +
86D GLN 4.8 6.5 + - - +
87D GLY* 4.1 2.9 - - - -
88D ASP* 3.1 26.1 + - - +
114D LEU* 5.7 2.6 - - - +
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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