Contacts of the strand formed by residues 64 - 73 (chain A) in PDB entry 5I4E
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 GLY 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PRO* 3.6 4.5 - - - +
60A SER 2.8 36.4 + - - +
61A GLU 4.3 0.6 + - - -
62A LEU 3.5 3.2 + - - -
63A HIS* 1.3 71.9 - - - +
65A PHE* 1.4 68.0 + - - -
122A LEU* 4.4 0.7 - - - -
709A PRO* 4.0 5.9 - - - +
710A ARG* 4.0 14.1 + - - +
713A LEU* 4.1 18.1 - - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 4.2 14.4 - - + -
58A VAL 3.3 18.6 - - - +
59A PRO* 4.0 14.6 - - + -
60A SER* 4.0 2.5 - - - +
63A HIS* 3.0 12.7 + - - +
64A GLY* 1.4 79.8 - - - +
66A GLU* 1.3 64.3 + - - +
95A GLN 5.5 0.2 - - - -
97A GLN* 3.4 33.7 - - + -
118A GLU* 3.9 24.0 - - + -
119A ALA* 3.4 41.5 - - + +
122A LEU* 3.7 15.2 - - + +
126A ARG* 4.0 8.5 + - - -
713A LEU* 4.0 21.1 - - + -
717A ARG* 5.1 3.1 - - - -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 3.5 9.2 - - - -
58A VAL* 2.9 38.1 + - + +
59A PRO 5.1 0.2 - - - +
60A SER* 3.1 30.5 + - - -
63A HIS* 4.6 12.8 - - + -
65A PHE* 1.3 76.3 - - - +
67A ALA* 1.3 65.8 + - - +
68A ALA 3.6 0.3 + - - -
82A LEU* 3.7 44.9 - - + +
84A GLU* 3.8 24.9 - - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.9 7.4 - - + -
56A VAL 3.5 7.0 - - - +
57A TRP* 3.5 19.7 - - + -
66A GLU* 1.3 76.6 - - - +
68A ALA* 1.3 59.4 + - - +
82A LEU* 3.9 6.6 - - - +
83A ALA* 3.1 35.2 + - + +
84A GLU 4.8 0.7 + - - -
99A MET* 4.9 12.1 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.4 6.4 - - - +
56A VAL* 2.7 42.0 + - + +
58A VAL* 3.7 30.1 - - + -
67A ALA* 1.3 76.4 - - - +
69A ALA* 1.3 58.9 + - - +
80A VAL* 3.9 13.0 - - + -
81A GLU 3.2 15.5 - - - +
82A LEU* 4.1 9.4 - - + -
83A ALA* 4.1 1.8 - - - +
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Residues in contact with ALA 69 (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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53A ARG 3.7 17.3 - - - +
54A ARG* 3.8 5.4 - - + -
55A LEU* 4.5 7.9 - - + +
68A ALA* 1.3 69.4 - - - +
70A LEU* 1.3 62.2 + - - +
71A ARG* 3.0 5.9 + - - -
80A VAL* 3.3 2.4 - - - -
81A GLU* 2.7 53.6 + - + +
83A ALA* 4.9 1.9 - - - +
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Residues in contact with LEU 70 (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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54A ARG* 2.7 81.8 + - + +
56A VAL* 4.1 20.0 - - + -
68A ALA 3.6 1.4 + - - -
69A ALA* 1.3 69.4 - - - +
71A ARG* 1.3 56.4 + - - +
72A ASP 3.8 18.6 - - - +
73A GLU* 4.1 20.4 - - + +
78A ALA* 4.4 12.3 - - + -
79A GLU 3.8 7.6 - - - +
80A VAL* 4.0 15.3 - - + -
93A ARG* 6.4 0.2 - - + -
96A ILE* 4.8 9.0 - - + -
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Residues in contact with ARG 71 (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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54A ARG* 3.4 8.9 + - - -
69A ALA* 3.0 6.3 + - - +
70A LEU* 1.3 72.8 - - - +
72A ASP* 1.3 62.9 + - + +
79A GLU* 2.9 53.4 + - - +
80A VAL* 4.2 6.1 - - - +
81A GLU* 4.8 11.6 + - + +
88A ARG* 4.0 30.6 - - - +
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Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 3.7 9.6 + - - +
70A LEU* 3.6 8.9 - - - +
71A ARG* 1.3 87.1 - - + +
73A GLU* 1.3 75.9 + - - +
78A ALA* 3.8 0.9 - - - -
79A GLU* 3.2 35.1 + - + +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 4.5 7.0 + - - +
70A LEU* 4.1 23.6 - - + +
72A ASP* 1.3 92.1 + - - +
74A GLY* 1.3 62.6 + - - +
77A GLU 4.5 1.8 - - - -
78A ALA* 4.7 2.5 - - + +
93A ARG* 2.9 39.2 + - + -
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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