Contacts of the strand formed by residues 63 - 69 (chain A) in PDB entry 3H44
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LYS* 4.2 10.5 - - - +
61A LYS 3.7 5.8 + - - +
62A ARG* 1.3 76.6 - - - +
64A TYR* 1.3 63.4 + - - +
78A ILE* 3.5 3.8 - - - +
79A SER* 2.8 50.0 + - - +
81A PRO* 5.9 3.1 - - - +
264A LEU* 3.7 18.2 - - + +
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Residues in contact with TYR 64 (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 HIS* 5.9 0.5 - - - -
54A ILE* 4.0 29.4 + - + +
56A LYS* 4.0 15.4 - - + +
60A ASP* 2.4 33.9 + - - -
62A ARG* 3.1 38.9 + - + -
63A GLU* 1.3 78.8 - - - +
65A ARG* 1.3 60.3 + - - +
76A LEU* 3.5 23.1 - - + -
77A LEU 3.3 4.0 - - - +
78A ILE* 3.7 26.5 - - + -
264A LEU* 3.5 10.1 - - - +
433A TYR* 2.8 25.6 + - - -
450A LEU* 3.8 21.8 - - + -
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Residues in contact with ARG 65 (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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50A ILE* 3.8 22.7 - - + +
51A GLY 5.6 0.7 - - - +
54A ILE* 4.3 1.3 - - - -
64A TYR* 1.3 74.3 - - - +
66A GLY* 1.3 72.0 + - - +
67A LEU* 4.9 4.3 - - + -
75A VAL 3.9 0.7 - - - +
76A LEU* 3.2 5.6 - - - +
77A LEU* 2.8 46.5 + - + +
264A LEU* 3.4 39.0 + - + +
265A ASP* 2.9 29.7 + - - +
268A THR* 3.1 31.4 + - - +
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Residues in contact with GLY 66 (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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50A ILE* 3.4 10.0 - - - +
51A GLY 3.0 19.8 + - - +
54A ILE* 3.9 14.3 - - - +
65A ARG* 1.3 76.0 - - - +
67A LEU* 1.3 66.6 + - - +
75A VAL 3.4 7.0 - - - -
76A LEU* 4.0 7.9 - - - -
446A LEU* 3.7 20.4 - - - -
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Residues in contact with LEU 67 (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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47A ILE* 4.1 23.3 - - + -
49A ARG 3.0 16.6 - - - +
50A ILE* 4.0 8.1 - - + -
65A ARG* 4.9 4.9 - - + -
66A GLY* 1.3 77.9 - - - +
68A GLU* 1.3 58.5 + - - +
69A LEU* 4.7 10.3 - - + -
74A LYS* 3.7 1.9 - - - -
75A VAL* 2.8 72.3 + - + +
77A LEU* 4.0 14.4 - - + -
268A THR* 4.1 29.8 - - + +
271A VAL* 6.0 0.9 - - + -
272A VAL* 5.7 0.4 - - + -
446A LEU* 3.4 14.8 - - - +
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Residues in contact with GLU 68 (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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47A ILE* 3.6 5.2 - - - +
48A LYS* 2.8 54.4 + - + +
49A ARG* 3.0 48.4 + - + +
67A LEU* 1.3 75.1 - - - +
69A LEU* 1.3 74.3 + - - +
72A GLY* 3.5 17.9 - - - +
73A ILE 3.4 10.3 - - - +
74A LYS* 4.5 16.2 - - + +
446A LEU* 4.6 0.6 - - + +
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Residues in contact with LEU 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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46A ALA 3.5 11.0 - - - +
47A ILE* 4.5 6.5 - - + -
48A LYS* 3.6 5.7 - - - +
67A LEU* 4.7 7.6 - - + -
68A GLU* 1.3 86.5 - - - +
70A ALA* 1.3 66.9 + - - +
71A ASN* 3.1 22.7 - - - +
72A GLY* 2.9 11.1 + - - -
73A ILE* 2.8 26.6 + - + +
75A VAL* 4.1 12.1 - - + -
271A VAL* 4.3 13.5 - - + +
272A VAL* 4.1 24.2 - - + -
275A PHE* 4.0 35.4 - - + +
276A SER* 4.4 7.4 - - - +
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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