Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 1EAW
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 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C ALA 3.5 0.2 - - - +
67C PHE* 3.4 3.1 - - - -
68C LEU* 2.7 57.8 + - + +
79C GLY 3.5 12.9 + - - +
80C VAL* 1.3 73.9 - - - +
82C GLU* 1.3 61.1 + - - +
83C ARG* 3.1 22.6 + - - +
112C ALA* 3.7 3.1 - - - -
113C GLU* 2.5 56.1 + - - +
115C SER* 4.3 5.3 + - - -
118C VAL* 3.5 20.2 - - + +
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Residues in contact with GLU 82 (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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65C THR* 3.5 27.0 + - + +
66C ALA 3.2 4.9 - - - +
67C PHE* 3.6 26.2 - - + +
76C ARG* 5.7 1.2 - - - -
80C VAL* 4.0 3.0 + - - +
81C GLN* 1.3 73.2 - - - +
83C ARG* 1.3 83.9 + - - +
84C ARG* 5.8 4.7 - - + +
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Residues in contact with ARG 83 (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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65C THR* 3.5 4.7 - - - -
66C ALA* 2.8 42.3 + - + +
68C LEU* 3.9 18.8 - - + -
81C GLN* 3.1 32.3 + - - +
82C GLU* 1.3 95.1 + - - +
84C ARG* 1.3 69.7 + - - +
85C LEU* 4.8 0.9 - - - +
108C LEU* 4.2 16.8 - - + -
110C LYS* 2.9 47.7 + - - +
111C PRO 3.2 21.6 + - - -
112C ALA* 3.6 3.0 - - - +
113C GLU* 3.9 11.3 + - - +
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Residues in contact with ARG 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PRO 5.6 0.4 - - - +
62C THR* 3.9 39.2 + - - +
64C TRP 4.0 9.6 + - - +
65C THR* 4.7 7.9 - - + +
82C GLU* 5.8 4.5 - - + +
83C ARG* 1.3 80.6 - - - +
85C LEU* 1.3 66.9 + - - +
108C LEU* 3.7 5.2 - - - -
109C GLU* 3.3 58.5 + - + +
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Residues in contact with LEU 85 (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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33C LEU* 4.0 19.3 - - + -
52C LEU* 4.9 5.4 - - + -
59C TYR* 5.2 0.7 - - + -
61C PRO* 3.6 30.9 + - + +
62C THR* 4.6 2.3 + - - +
64C TRP* 3.6 37.8 + - + +
66C ALA* 4.9 3.6 - - + -
83C ARG 4.8 1.6 - - - +
84C ARG* 1.3 83.9 + - - +
86C LYS* 1.3 61.8 + - - +
87C ARG 4.5 3.8 - - - +
88C ILE* 5.0 4.7 - - + -
106C LEU* 3.9 34.3 - - + -
107C GLU 3.1 18.2 - - - +
108C LEU* 4.0 19.5 - - + -
109C GLU* 4.4 4.9 - - - +
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Residues in contact with LYS 86 (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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61C PRO* 4.0 9.1 - - - +
85C LEU* 1.3 68.3 - - - +
87C ARG* 1.3 61.6 + - + +
107C GLU* 2.3 49.6 + - - +
108C LEU 3.1 23.7 - - - +
109C GLU* 3.0 35.8 + - + +
110C LYS* 4.6 3.8 - - - +
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Residues in contact with ARG 87 (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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51C TRP* 3.6 17.9 - - - -
61C PRO* 4.0 8.9 - - - +
85C LEU* 3.6 1.9 - - - +
86C LYS* 1.3 85.4 - - + +
88C ILE* 1.3 76.6 + - - +
89C ILE* 3.8 23.3 - - + +
105C LEU 3.7 0.7 - - - +
106C LEU* 3.4 3.5 - - - +
107C GLU* 2.7 68.1 + - + +
241C ASN 5.2 3.4 + - - -
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Residues in contact with ILE 88 (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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59C TYR* 4.0 37.5 - - + -
60C SER* 3.3 35.0 - - + -
61C PRO* 3.9 24.0 - - + +
64C TRP* 4.1 5.6 - - + -
85C LEU* 5.0 4.7 - - + -
87C ARG* 1.3 82.9 - - - +
89C ILE* 1.3 70.6 + - - +
90C SER* 3.9 5.5 + - - +
104C ALA* 4.4 7.4 - - + -
105C LEU 3.3 2.9 - - - +
106C LEU* 3.4 27.1 - - + -
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Residues in contact with ILE 89 (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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51C TRP* 3.8 32.1 - - + -
87C ARG* 3.8 29.6 - - + +
88C ILE* 1.3 79.5 - - - +
90C SER* 1.3 69.1 + - - +
92C PRO* 5.4 2.0 - - + -
104C ALA* 3.1 7.0 - - - -
105C LEU* 2.8 39.3 + - + +
237C TRP* 3.8 11.6 - - + -
241C ASN* 3.9 33.4 - - + +
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Residues in contact with SER 90 (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 ALA* 5.1 5.2 - - - -
59C TYR* 5.5 7.6 - - - -
88C ILE* 3.9 6.9 + - - +
89C ILE* 1.3 81.8 - - - +
91C HIS* 1.3 74.4 + - - +
92C PRO* 3.1 11.1 - - - +
94C PHE* 4.1 17.6 - - - +
103C ILE 3.9 0.7 - - - -
104C ALA* 3.7 13.4 - - - +
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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