Contacts of the strand formed by residues 26 - 33 (chain I) in PDB entry 3STJ
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 26 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL* 4.3 8.7 - - + +
23I LEU* 3.0 8.8 + - - +
24I PRO 3.2 3.1 - - - +
25I ALA* 1.4 82.1 - - + +
27I VAL* 1.3 66.6 + - - +
67I GLY 3.5 15.5 - - - +
68I VAL* 4.9 4.3 - - + -
95I ASN 4.7 8.5 + - - -
127I ILE* 5.0 3.6 - - + -
144I VAL* 3.7 44.2 - - + +
145I GLY* 4.5 4.7 - - - +
152I GLN* 3.0 27.0 - - + +
189I GLY* 4.9 1.3 - - - -
190I ALA* 3.8 26.7 - - + +
192I LEU* 5.2 4.0 - - + -
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Residues in contact with VAL 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I PRO 4.5 1.1 - - - +
26I VAL* 1.3 80.6 - - - +
28I SER* 1.3 58.9 + - - +
29I VAL* 4.3 1.1 - - + -
66I SER* 3.3 8.0 - - - -
67I GLY* 2.8 54.3 + - - +
68I VAL 4.4 0.2 - - - +
69I ILE* 3.6 23.8 - - + -
77I VAL* 3.9 17.3 - - + -
92I ILE* 3.9 23.1 - - + -
93I GLN 3.6 9.0 - - - +
94I LEU* 3.6 29.4 - - + -
146I ASN* 5.3 0.2 - - - -
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Residues in contact with SER 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I VAL* 1.3 72.3 - - - +
29I VAL* 1.3 63.0 + - - +
30I ARG* 4.0 2.0 + - - -
64I LEU* 4.8 5.4 - - - -
65I GLY 3.8 5.6 - - - -
66I SER* 4.4 0.4 - - - +
91I SER 3.7 0.7 - - - +
92I ILE* 3.2 8.3 - - - +
93I GLN* 2.9 55.4 + - - -
146I ASN* 2.4 34.2 + - - -
151I GLY* 5.2 1.0 - - - -
152I GLN* 5.0 2.3 + - - +
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Residues in contact with VAL 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I VAL* 4.3 0.9 - - + -
28I SER* 1.3 77.2 - - - +
30I ARG* 1.3 59.9 + - - +
31I VAL* 4.1 4.0 + - + -
63I GLY 3.9 0.3 - - - +
64I LEU* 3.5 6.9 - - - +
65I GLY 2.9 36.8 + - - +
66I SER 3.5 28.0 - - - +
67I GLY* 3.8 9.0 - - - +
77I VAL* 4.7 0.9 - - + -
79I THR* 4.5 1.8 - - - +
83I VAL* 4.0 9.6 - - + +
84I ILE* 3.7 30.5 - - + -
90I ILE* 4.0 15.5 - - + -
91I SER 3.5 2.0 - - - -
92I ILE* 4.0 16.8 - - + -
116I LEU* 4.3 7.2 - - + -
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I SER* 4.0 2.4 - - - -
29I VAL* 1.3 72.1 - - - +
31I VAL* 1.3 69.0 + - - +
32I GLU* 5.2 9.0 + - + +
62I GLU* 3.1 35.4 + - + +
63I GLY 3.6 7.6 - - - +
64I LEU* 4.8 16.3 - - + +
89I LYS 4.0 0.2 - - - +
90I ILE* 3.4 3.8 - - - +
91I SER* 2.8 56.3 + - - +
93I GLN* 6.6 0.2 - - + -
99I GLU* 6.3 0.6 - - - -
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Residues in contact with VAL 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I VAL* 4.3 7.2 - - + +
30I ARG* 1.3 80.0 - - - +
32I GLU* 1.3 65.1 - - - +
61I PHE* 3.7 24.9 - - + -
62I GLU* 3.3 6.4 - - - +
63I GLY* 2.8 39.1 + - - +
83I VAL* 3.7 26.2 - - + +
84I ILE* 3.9 12.3 - - + -
86I GLN 5.8 0.2 - - - +
87I ALA* 3.7 32.3 - - + +
89I LYS 3.4 2.7 - - - -
90I ILE* 3.9 12.1 - - + -
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Residues in contact with GLU 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ARG* 5.2 11.0 + - + +
31I VAL* 1.3 80.8 - - - +
33I GLY* 1.3 53.2 + - - +
61I PHE 3.4 4.7 - - - +
62I GLU* 3.1 34.2 - - + +
87I ALA 3.7 0.2 - - - -
88I GLN* 2.7 31.1 + - - +
89I LYS* 2.9 44.7 + - + +
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Residues in contact with GLY 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I GLU* 1.3 75.8 - - - +
34I THR* 1.4 60.1 + - - -
60I PRO* 3.3 23.4 - - - +
61I PHE* 3.2 26.5 + - - -
86I GLN 3.6 9.9 - - - -
88I GLN* 3.7 19.2 - - - +
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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