Contacts of the strand formed by residues 20 - 27 (chain H) in PDB entry 3Q3G
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 VAL 20 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12H GLU* 3.6 41.3 - - + +
14H VAL* 3.9 14.4 - - + -
19H SER* 1.3 75.9 - - - +
21H LYS* 1.4 62.2 + - - +
22H LEU* 3.9 12.1 - - + -
83H LEU 3.7 1.0 - - - +
84H GLN* 3.2 5.8 - - - +
85H LEU* 2.9 59.6 + - + -
88H LEU* 3.8 20.2 - - + -
120H VAL* 4.4 7.6 - - + -
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Residues in contact with LYS 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H SER* 4.8 1.6 + - - -
12H GLU* 4.1 11.6 + - - +
20H VAL* 1.4 73.8 - - - +
22H LEU* 1.3 65.5 + - - +
23H SER* 4.2 1.2 + - - -
71H THR 5.9 0.4 - - - -
73H THR* 4.0 13.1 + - - +
82H TYR* 3.7 40.4 - - + -
83H LEU 3.4 9.2 - - - +
84H GLN* 3.9 28.8 + - + +
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Residues in contact with LEU 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H SER* 3.7 7.4 - - - +
12H GLU* 3.9 22.9 - - + +
20H VAL* 3.9 14.6 - - + -
21H LYS* 1.3 72.6 - - - +
23H SER* 1.3 60.7 + - - +
38H TRP* 4.1 15.2 - - + -
82H TYR* 3.2 7.8 - - - +
83H LEU* 2.8 49.0 + - + +
85H LEU* 4.5 2.7 - - + -
96H TYR* 3.7 33.2 - - + -
118H THR* 3.9 17.3 - - + -
120H VAL* 3.8 30.3 - - + -
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Residues in contact with SER 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLN 4.6 0.4 + - - -
8H GLN* 3.5 7.0 + - - +
9H SER* 3.0 46.6 + - - -
21H LYS 4.2 1.1 + - - -
22H LEU* 1.3 74.5 - - - +
24H CYS* 1.3 61.0 + - - +
25H THR* 4.8 3.1 + - - -
38H TRP* 4.1 4.1 - - - -
80H THR* 3.7 19.1 - - - +
81H ALA 3.5 4.7 - - - -
82H TYR* 3.7 15.0 - - - -
118H THR* 4.9 0.2 + - - -
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Residues in contact with CYS 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 4.0 13.7 - - - -
7H GLN 3.4 5.6 - - - -
8H GLN* 4.1 2.2 - - + -
23H SER* 1.3 77.0 - - - +
25H THR* 1.3 61.6 + - - +
26H PRO* 4.0 3.5 - - - +
36H MET* 4.0 18.6 - - + +
38H TRP* 3.8 10.1 - - + -
80H THR* 3.4 1.1 - - - -
81H ALA* 2.8 38.2 + - + +
98H CYS* 2.0 54.3 - - + -
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Residues in contact with THR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H LEU* 4.6 0.7 - - - -
7H GLN* 2.8 43.9 + - - +
23H SER* 4.8 2.9 + - - -
24H CYS* 1.3 70.9 + - - +
26H PRO* 1.4 70.3 - - - +
27H SER* 3.6 0.9 + - - -
78H SER 3.7 8.1 - - - +
79H ASN* 3.2 18.8 - - + +
80H THR* 2.7 27.6 + - - +
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Residues in contact with PRO 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H GLN 3.5 6.3 - - - +
6H LEU* 3.5 26.2 - - + -
24H CYS 4.0 3.8 - - - +
25H THR* 1.4 87.9 - - - +
27H SER* 1.3 59.4 - - - +
28H GLY 4.0 0.2 + - - -
29H PHE* 3.6 33.2 - - + +
31H ILE* 3.5 23.6 - - + -
36H MET* 3.8 4.9 - - + -
79H ASN* 3.0 45.4 + - - +
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Residues in contact with SER 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H GLN* 3.6 16.9 + - - -
4H VAL* 3.4 6.8 - - - +
5H GLN* 2.9 38.6 + - - +
7H GLN* 5.5 4.8 + - - +
25H THR 3.6 2.8 + - - -
26H PRO* 1.3 71.2 - - - +
28H GLY* 1.3 59.3 + - - +
29H PHE* 3.6 0.9 - - - -
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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