Contacts of the strand formed by residues 31 - 38 (chain A) in PDB entry 5T4S
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 GLN 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE 2.7 42.0 + - - +
29A PRO* 4.2 5.8 + - + +
30A PRO* 1.3 73.9 - - - +
32A THR* 1.3 60.0 + - - +
33A PHE* 3.3 19.3 - - + -
62A LYS* 5.2 8.4 - - - +
63A LEU 3.5 5.9 - - - +
64A PHE* 3.4 22.6 - - - -
65A ASP* 2.8 51.7 + - - +
68A ASP* 3.9 21.2 + - + +
69A SER* 4.3 3.6 - - - -
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Residues in contact with THR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 4.3 20.5 - - + +
24A ILE 3.2 10.3 - - - +
25A GLY* 4.7 6.1 - - - -
30A PRO* 4.1 11.6 + - + +
31A GLN* 1.3 73.7 - - - +
33A PHE* 1.3 61.2 + - - +
62A LYS* 2.9 49.6 + - - +
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLY 3.4 3.6 - - - +
23A GLU* 3.4 6.2 - - - -
24A ILE* 2.9 35.3 + - + +
26A ILE* 3.6 27.4 - - + -
31A GLN* 3.3 34.1 - - + -
32A THR* 1.3 73.9 - - - +
34A LYS* 1.3 63.0 + - - +
35A VAL* 3.7 8.5 + - + -
46A VAL* 3.7 30.3 - - + -
62A LYS* 3.4 41.5 - - + -
63A LEU 3.7 3.6 - - - -
64A PHE* 3.3 38.4 - - + -
125A ASP* 3.8 9.4 - - + +
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.7 35.2 + - + -
22A GLY 3.3 5.8 - - - -
23A GLU* 3.5 17.3 - - - +
33A PHE* 1.3 70.7 - - - +
35A VAL* 1.3 60.3 + - - +
62A LYS* 6.4 0.2 - - - -
123A GLU* 3.8 25.5 + - - +
124A PHE* 3.9 9.4 - - - -
125A ASP* 2.7 47.2 + - - +
126A GLY 3.0 7.4 + - - -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.2 9.2 - - - +
22A GLY 2.8 41.2 + - - +
24A ILE* 3.7 43.1 - - + -
33A PHE* 4.2 7.6 - - + -
34A LYS* 1.3 78.8 - - - +
36A VAL* 1.3 61.0 + - - +
37A PHE* 3.6 21.4 - - + -
46A VAL* 4.3 4.7 - - + -
124A PHE* 4.4 0.4 - - - -
126A GLY* 3.2 23.6 - - - +
127A VAL 4.1 2.5 - - - +
128A VAL* 3.8 15.5 - - + +
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Residues in contact with VAL 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR 3.6 11.9 - - - +
21A TYR* 4.4 1.6 - - + -
35A VAL* 1.3 73.4 - - - +
37A PHE* 1.3 70.2 + - - +
38A ASP* 4.2 1.8 - - + -
124A PHE* 3.5 39.5 - - + -
126A GLY 3.0 10.5 + - - +
127A VAL* 3.4 7.4 - - + +
128A VAL 2.7 32.3 + - - +
227A THR 4.6 0.7 - - - +
228A GLY* 4.0 4.9 - - - -
402A PG6 3.9 18.6 - - - -
403A DMS 3.4 38.4 - - - +
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Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.0 21.1 - - + -
12A LEU* 4.1 6.1 - - + -
20A TYR 4.5 2.6 + - - -
22A GLY* 4.1 9.9 - - - -
24A ILE* 3.8 13.0 - - + -
35A VAL* 3.6 35.0 - - + -
36A VAL* 1.3 71.8 - - - +
38A ASP* 1.3 53.8 + - - +
99A VAL* 3.8 23.6 - - + -
128A VAL* 3.3 33.7 - - + -
130A MET* 4.0 14.4 - - + -
160A PHE* 3.4 16.9 - - + -
162A TYR* 3.9 2.5 + - - -
176A ILE* 3.4 33.7 - - + -
178A LEU* 5.9 2.5 - - + -
227A THR* 2.8 27.0 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.2 4.3 - - + -
37A PHE* 1.3 72.7 - - - +
39A THR* 1.3 55.3 + - - +
40A GLY* 2.7 25.4 + - - -
41A SER* 2.6 35.3 + - - +
83A TYR* 4.0 6.8 - - - -
127A VAL* 3.8 19.5 - - + -
128A VAL 2.9 8.7 + - - -
129A GLY* 3.4 0.9 - - - -
130A MET* 2.7 27.3 + - - +
226A ASP* 2.8 18.4 - - - +
227A THR* 3.4 1.6 - - - -
228A GLY* 3.4 15.3 + - - +
402A PG6 3.9 12.8 - - - +
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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