Contacts of the strand formed by residues 68 - 75 (chain A) in PDB entry 4HC1
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ALA 3.7 1.8 + - - -
67A ALA* 1.3 75.6 - - - +
69A THR* 1.3 61.4 + - - -
70A ARG* 5.2 2.5 - - - -
86A GLN* 3.1 13.6 + - - +
87A LEU* 2.9 36.1 + - - +
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Residues in contact with THR 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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10A GLU* 3.8 6.9 + - - -
41A LEU* 5.3 5.5 - - - +
68A GLY* 1.3 73.0 - - - -
70A ARG* 1.3 70.2 + - - +
71A VAL* 4.2 15.3 + - + +
84A THR* 3.4 28.5 - - + +
85A VAL 3.9 3.6 - - - -
86A GLN* 3.5 13.4 + - - -
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Residues in contact with ARG 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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23A LEU* 4.7 1.1 - - + -
38A TRP* 3.7 22.5 - - + +
39A ARG 4.7 10.7 + - - +
40A GLY* 5.6 0.6 - - - -
41A LEU* 3.2 42.7 - - - +
43A THR* 5.3 1.0 + - - -
44A SER* 5.5 6.5 + - - -
57A LEU* 3.1 44.3 - - + +
59A VAL* 5.0 4.2 - - - +
66A ALA* 3.1 39.2 + - - +
67A ALA 5.5 0.2 - - - -
68A GLY 3.8 1.8 + - - +
69A THR* 1.3 79.8 - - - +
71A VAL* 1.3 62.2 - - - +
84A THR* 3.7 2.8 - - - +
85A VAL* 3.1 41.1 + - + +
87A LEU* 4.4 22.2 - - + +
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Residues in contact with VAL 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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38A TRP* 3.5 5.8 - - - -
39A ARG* 2.9 64.0 + - + +
69A THR* 4.2 14.1 + - + +
70A ARG* 1.3 79.1 - - - +
72A CYS* 1.3 66.6 + - - +
73A VAL* 3.9 17.9 + - + -
82A GLN* 3.8 26.9 - - + +
83A HIS 4.0 4.9 - - - +
84A THR* 4.1 14.6 - - - +
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Residues in contact with CYS 72 (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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25A CYS* 2.0 58.0 - - + -
36A VAL* 3.7 15.0 - - - -
37A GLN 3.3 12.3 - - - -
38A TRP* 4.0 16.8 - - + -
70A ARG 4.2 0.2 + - - -
71A VAL* 1.3 73.4 - - - +
73A VAL* 1.3 61.6 + - - +
74A GLY 4.1 0.2 + - - -
81A PHE 3.9 0.2 - - - +
82A GLN* 3.3 5.0 - - - -
83A HIS* 3.1 38.1 + - + +
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Residues in contact with VAL 73 (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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35A SER 4.7 0.3 - - - -
36A VAL* 3.4 3.3 - - - -
37A GLN* 2.7 47.4 + - + +
39A ARG* 4.1 26.0 - - + +
71A VAL* 3.9 18.4 - - + -
72A CYS* 1.3 77.6 - - - +
74A GLY* 1.3 65.8 + - - +
75A SER* 6.0 0.9 - - - -
80A THR* 5.2 9.6 - - + -
81A PHE 3.4 8.5 - - - +
82A GLN* 4.4 7.2 - - + +
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Residues in contact with GLY 74 (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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27A LEU* 3.9 16.4 - - - -
35A SER 3.2 9.0 - - - -
36A VAL* 4.0 5.4 - - - +
72A CYS 4.1 0.4 + - - -
73A VAL* 1.3 77.6 - - - +
75A SER* 1.3 59.1 + - - -
79A ARG 3.7 0.4 - - - +
80A THR* 3.1 5.0 - - - -
81A PHE* 2.7 44.1 + - - +
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Residues in contact with SER 75 (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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27A LEU* 3.6 5.4 - - - +
33A GLY 4.5 6.8 + - - -
34A ALA* 3.4 4.0 - - - -
35A SER* 2.6 51.2 + - - +
73A VAL* 6.0 0.9 - - - -
74A GLY* 1.3 75.2 - - - -
76A CYS* 1.3 63.2 + - - +
78A GLY* 4.3 8.5 + - - -
79A ARG 3.2 13.2 + - - -
80A THR* 4.3 13.2 - - - +
81A PHE* 5.4 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