Contacts of the strand formed by residues 35 - 40 (chain T) in PDB entry 4C4K
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 GLU 35 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33T THR 3.8 1.2 + - - -
34T PRO* 1.3 74.7 - - - +
36T VAL* 1.3 62.8 + - - +
37T THR* 5.0 8.6 + - - +
80T SER 3.7 0.5 - - - +
81T LEU* 3.4 7.3 - - - -
82T GLY* 3.0 43.1 + - - +
1102T EDO 3.7 6.3 - - - -
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Residues in contact with VAL 36 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T PHE* 3.7 33.7 - - + -
34T PRO 4.1 2.0 - - - +
35T GLU* 1.3 76.6 - - - +
37T THR* 1.3 66.6 + - - +
38T TRP* 4.1 8.1 - - + -
44T LYS* 4.6 10.2 + - - -
55T ILE* 5.2 0.2 - - + -
57T ASN* 3.5 36.0 + - - +
62T THR* 3.6 11.7 - - - +
79T LEU* 3.8 15.9 - - + -
80T SER 3.7 2.9 - - - -
81T LEU* 3.8 12.6 - - + -
1102T EDO 4.0 14.4 + - - +
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Residues in contact with THR 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T GLU* 5.0 9.9 + - - +
36T VAL* 1.3 76.7 + - - +
38T TRP* 1.3 69.7 + - - +
39T SER* 4.5 6.0 + - - -
44T LYS* 3.8 36.5 + - + +
78T THR 3.4 3.1 - - - +
79T LEU* 3.4 2.7 - - - +
80T SER* 2.8 51.0 + - - -
1101T EDO 4.1 17.1 + - - +
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Residues in contact with TRP 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T LEU* 4.2 20.0 - - + -
24T VAL* 4.5 11.2 - - + -
26T CYS* 4.9 2.0 - - + -
36T VAL* 4.1 8.3 + - + -
37T THR* 1.3 73.2 - - - +
39T SER* 1.3 59.0 + - - +
44T LYS* 3.5 7.4 - - - +
45T ILE* 2.8 35.7 + - + +
55T ILE* 3.8 41.2 - - + +
62T THR* 2.9 41.4 + - + +
64T LEU* 4.0 48.1 - - + +
77T TYR* 4.4 13.2 - - + -
78T THR 3.2 20.2 - - - -
79T LEU* 3.9 28.7 - - + -
92T VAL* 4.5 9.6 - - + -
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Residues in contact with SER 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T THR* 4.5 8.7 - - - +
38T TRP* 1.3 76.0 - - - +
40T CYS* 1.3 60.2 - - - +
41T GLY 4.1 0.6 + - - -
42T GLY* 4.6 7.6 + - - -
43T ARG 3.2 25.8 - - - -
44T LYS* 4.1 2.5 - - - -
45T ILE* 3.8 7.4 - - - +
76T LEU 4.0 0.3 - - - +
77T TYR* 3.5 6.9 - - - -
78T THR* 2.8 53.9 + - - +
80T SER* 5.1 2.4 + - - -
1101T EDO 5.3 2.2 - - - -
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Residues in contact with CYS 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39T SER* 1.3 73.7 - - - +
41T GLY* 1.3 67.4 + - - +
42T GLY 3.4 0.9 - - - -
43T ARG* 2.9 30.5 + - - +
45T ILE* 4.0 18.6 - - + +
75T GLY* 6.5 0.9 - - - -
76T LEU 4.0 14.4 - - - +
77T TYR* 4.9 7.9 - - + -
1099T EDO 4.2 16.2 - - - +
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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