Contacts of the strand formed by residues 52 - 58 (chain C) in PDB entry 3E5X
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 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C ILE* 3.6 8.5 - - - +
51C THR* 1.3 81.3 + - - +
53C MET* 1.3 65.3 + - - +
54C ILE* 3.9 2.9 + - - +
84C ILE 4.3 0.2 - - - +
86C LYS* 2.9 24.6 + - - +
87C LEU* 3.8 2.2 - - - -
106C TRP* 3.7 35.1 - - - +
107C PHE 3.3 16.4 + - - -
108C SER* 4.2 8.5 + - - -
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Residues in contact with MET 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C SER* 1.3 72.7 - - - +
54C ILE* 1.3 60.4 + - - +
55C PHE 4.0 0.7 - - - -
83C LEU* 3.9 32.1 - - + -
84C ILE 3.2 11.7 - - - +
85C GLY* 4.2 6.3 - - - -
87C LEU* 3.8 15.4 - - + +
105C CYS 3.6 0.5 - - - +
106C TRP* 3.4 2.8 - - - -
107C PHE* 2.7 44.5 + - + +
112C LEU* 3.9 23.1 - - + -
126C ILE* 3.8 18.2 - - + -
130C TYR* 3.3 23.8 - - + +
127D PHE* 3.7 33.9 - - + -
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 4.4 3.6 - - + -
44C ILE* 4.1 13.5 - - + -
50C ILE* 4.1 15.3 - - + -
52C SER 4.1 4.3 - - - +
53C MET* 1.3 76.2 - - - +
55C PHE* 1.3 61.3 + - - +
56C LEU* 3.9 1.3 + - - +
61C ILE* 5.3 0.2 - - + -
82C SER 3.9 0.3 - - - +
83C LEU* 3.6 4.3 - - - -
84C ILE* 2.9 66.0 + - + +
104C THR* 3.6 35.9 - - + -
105C CYS 3.4 2.2 - - - -
106C TRP* 3.7 50.3 - - + +
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Residues in contact with PHE 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.1 28.3 - - + -
25C LEU* 3.6 25.1 - - + -
26C ARG* 3.7 31.9 - - + -
29C THR* 4.1 11.0 - - + -
53C MET 4.0 0.2 - - - -
54C ILE* 1.3 73.9 - - - +
56C LEU* 1.3 64.8 + - - +
57C VAL* 3.5 20.4 + - + -
81C ASN* 3.6 36.3 - - - -
82C SER 3.5 12.8 - - - -
83C LEU* 3.9 8.7 - - + +
104C THR* 3.2 6.6 - - - -
105C CYS* 2.7 43.9 + - + +
107C PHE* 3.7 15.0 - + + -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 3.9 1.3 + - + +
55C PHE* 1.3 72.8 - - - +
57C VAL* 1.3 62.0 + - - +
58C GLU 3.4 36.8 - - - +
59C GLY 3.5 12.6 - - - +
61C ILE* 3.7 35.0 - - + +
78C ALA* 3.3 38.4 - - + +
79C GLY 3.3 20.6 - - - +
80C GLY 3.6 0.2 - - - -
81C ASN* 2.6 33.6 + - - -
82C SER 2.8 17.8 + - - +
84C ILE* 6.0 2.0 - - + -
102C THR* 3.8 7.2 - - + -
103C ARG 3.9 2.2 - - - -
104C THR* 4.7 1.1 - - - +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ARG* 2.8 49.1 + - + +
29C THR* 4.2 15.7 - - + -
34C ILE* 4.5 4.0 - - + -
55C PHE* 4.0 18.2 - - + -
56C LEU* 1.3 73.8 - - - +
58C GLU* 1.3 74.2 + - - +
80C GLY* 4.0 6.3 - - - -
103C ARG* 2.9 28.2 + - + +
104C THR 4.0 17.9 - - - +
105C CYS* 4.1 1.8 - - + +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ARG* 5.4 3.8 + - - +
56C LEU* 3.4 8.8 - - - +
57C VAL* 1.3 87.7 - - + +
59C GLY* 1.3 57.9 + - - +
80C GLY* 4.7 2.9 - - - -
101C PRO 4.4 3.4 - - - +
102C THR* 3.2 1.7 - - - -
103C ARG* 2.8 64.3 + - + +
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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