Contacts of the strand formed by residues 62 - 67 (chain C) in PDB entry 3EHW
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 62 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B PHE* 3.8 10.2 - - - -
118B LYS* 4.6 20.3 + - - -
58C ILE* 3.4 6.7 - - + +
59C PRO* 3.1 42.0 + - + +
60C PRO 3.0 6.1 - - - +
61C MET* 1.3 83.4 - - - +
63C LYS* 1.3 90.0 + - - +
114C PHE* 3.7 1.4 - - - -
115C ASN 2.8 25.7 + - - +
39Y THR* 6.1 1.2 - - - +
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA 3.6 14.6 - - - +
90B ALA* 2.8 27.3 + - - +
91B LYS 4.1 6.5 + - - -
92B HIS 4.4 1.8 - - - -
93B PHE* 3.6 45.1 - - + +
58C ILE* 4.2 5.5 - - - +
59C PRO* 5.6 0.9 - - - +
62C GLU* 1.3 98.1 + - - +
64C ALA* 1.3 65.6 + - - +
65C VAL* 6.5 0.7 - - + -
112C VAL* 5.1 2.7 - - + -
113C LEU 3.1 13.7 - - - +
114C PHE* 3.7 16.4 - - + -
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Residues in contact with ALA 64 (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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56C TYR* 4.3 21.1 - - + -
57C THR 6.0 0.4 - - - +
58C ILE* 3.9 26.8 - - + +
63C LYS* 1.3 79.1 - - - +
65C VAL* 1.3 64.0 + - - +
66C VAL* 3.7 2.0 + - + -
111C VAL 3.4 1.2 - - - +
112C VAL* 3.6 3.1 - - - +
113C LEU* 2.9 32.7 + - - +
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Residues in contact with VAL 65 (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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158A PHE* 3.8 27.8 - - + -
90B ALA* 3.7 33.0 - - + +
56C TYR* 3.5 17.8 + - - -
63C LYS* 6.5 0.7 - - + -
64C ALA* 1.3 74.6 - - - +
66C VAL* 1.3 63.0 + - - +
67C LYS* 3.5 6.6 + - + +
110C GLY* 4.1 15.9 - - - -
111C VAL 3.4 4.9 - - - +
112C VAL* 4.2 9.9 - - + -
152X GLU* 3.7 5.7 - - - +
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Residues in contact with VAL 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR 5.4 0.2 - - - +
52C SER* 3.3 40.6 - - - +
56C TYR* 3.5 25.1 - - + -
58C ILE* 4.9 0.2 - - + -
64C ALA* 4.6 5.4 - - + +
65C VAL* 1.3 71.9 - - - +
67C LYS* 1.3 63.8 + - - +
68C THR* 3.7 1.2 + - + -
109C VAL 3.9 0.2 - - - +
110C GLY* 3.3 4.0 - - - -
111C VAL* 2.7 48.3 + - + +
113C LEU* 3.8 29.8 - - + -
123C VAL* 4.6 4.7 - - + -
129C ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 67 (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* 4.2 0.2 + - - -
53C ALA* 3.0 25.2 + - - +
54C TYR* 3.7 23.4 + - + -
56C TYR* 2.9 10.6 + - - +
65C VAL* 4.5 8.1 - - + +
66C VAL* 1.3 75.9 - - - +
68C THR* 1.3 60.6 + - - +
69C ASP* 3.9 10.9 + - - +
108C ASN* 3.8 22.2 - - + +
109C VAL 4.2 2.9 - - - -
110C GLY* 4.8 2.5 - - - -
152X GLU* 2.7 50.7 + - - +
153X ARG 4.8 2.8 + - - -
154X GLY* 5.9 0.2 - - - -
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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