Contacts of the strand formed by residues 67 - 73 (chain A) in PDB entry 1SIW
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 LEU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.1 7.6 - - - +
64A LYS 2.8 32.7 + - - +
65A ASN* 3.8 13.9 - - + +
66A GLY* 1.3 87.1 - - - +
68A VAL* 1.3 65.1 + - - +
69A THR* 3.4 5.0 + - + +
103A TYR* 3.5 37.2 - - + +
813A VAL* 5.0 1.6 - - - -
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Residues in contact with VAL 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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61A ILE* 4.0 24.2 - - + -
62A TYR 3.5 6.5 - - - +
63A VAL* 4.3 1.8 - - + +
67A LEU* 1.3 70.6 - - - +
69A THR* 1.3 62.1 + - - +
70A TRP 4.4 3.6 - - - +
99A SER* 4.2 20.5 - - - +
102A LEU* 3.4 34.5 - - + -
103A TYR* 2.8 24.7 + - - +
792A TYR* 4.1 20.9 - - + +
812A ALA* 4.2 6.5 - - + -
813A VAL* 4.2 20.2 - - + +
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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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38A ARG* 4.7 12.8 + - - +
62A TYR* 2.9 14.0 + - - +
64A LYS* 3.8 36.0 - - + +
67A LEU* 3.9 9.6 - - + +
68A VAL* 1.3 77.4 - - - +
70A TRP* 1.3 96.5 + - + +
99A SER* 4.1 12.0 + - - -
28B ASN* 4.6 7.4 - - - +
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Residues in contact with TRP 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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38A ARG* 3.3 55.4 - - - -
39A TRP* 3.5 44.0 - + - -
40A GLN 4.6 0.7 - - - -
41A HIS* 4.5 2.0 - + + -
61A ILE* 3.9 0.9 - - - -
62A TYR* 2.9 68.4 + + + +
64A LYS* 4.2 8.3 - - + -
68A VAL* 4.4 4.3 - - - +
69A THR* 1.3 108.9 + - - +
71A GLU* 1.3 78.5 + - - +
72A THR* 4.1 3.8 - - + -
99A SER* 4.1 4.7 - - - -
28B ASN* 3.9 22.4 - - + -
29B VAL* 3.8 26.5 - - + -
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Residues in contact with GLU 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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59A TRP* 3.5 27.5 - - + -
60A LYS 3.1 16.4 - - - +
61A ILE* 4.5 7.2 - - + -
62A TYR* 3.9 1.3 - - - -
70A TRP* 1.3 79.1 - - - +
72A THR* 1.3 68.8 + - - +
95A GLY 3.5 7.0 - - - +
96A ALA 3.1 19.8 - - - +
99A SER* 2.8 44.4 + - - -
792A TYR* 2.8 29.0 + - + +
25B THR* 4.1 11.4 - - - +
28B ASN* 3.5 5.7 + - - +
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Residues in contact with THR 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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39A TRP* 4.9 4.7 - - + -
59A TRP* 3.4 8.7 - - - -
60A LYS* 2.8 37.6 + - - +
62A TYR* 2.7 35.4 + - + +
70A TRP* 4.1 9.6 - - + +
71A GLU* 1.3 79.5 - - - +
73A GLN* 1.3 66.2 + - - +
25B THR* 5.1 1.1 - - - -
29B VAL* 5.4 0.7 - - + -
250B ARG* 6.2 2.2 - - - +
258B VAL* 4.3 15.7 - - + -
261B GLU* 5.2 6.9 + - - -
262B THR* 3.9 20.6 - - + -
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Residues in contact with GLN 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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57A CYS* 5.7 0.2 - - + -
58A SER 4.0 4.3 - - - +
59A TRP* 3.4 35.7 - - + -
60A LYS* 4.0 11.1 + - - +
72A THR* 1.3 79.5 + - - +
74A GLN* 1.3 61.9 + - - +
75A THR* 3.8 8.3 + - - +
89A PRO* 3.2 35.9 - - + +
90A ARG 2.9 20.5 + - - +
91A GLY* 4.0 3.7 - - - +
21B THR* 4.0 6.4 - - - +
25B THR* 4.5 0.5 - - - +
261B GLU* 5.2 6.8 - - - +
262B THR* 3.0 50.4 + - - +
264B VAL* 3.7 6.7 - - - +
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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