Contacts of the strand formed by residues 26 - 33 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22K VAL* 4.5 7.6 - - + +
23K LEU* 3.0 14.1 + - - +
24K PRO* 4.0 3.5 - - - +
25K ALA* 1.3 80.4 - - + +
27K VAL* 1.3 65.2 + - - +
67K GLY 3.4 15.7 - - - +
68K VAL* 4.6 4.9 - - + +
95K ASN 4.8 6.1 + - - -
127K ILE* 5.0 3.4 - - + -
144K VAL* 3.8 43.7 - - + +
145K GLY* 4.6 3.1 - - - +
152K GLN* 2.9 26.0 - - + +
189K GLY* 4.7 2.0 - - - -
190K ALA* 3.7 28.3 - - + +
192K LEU* 5.2 4.3 - - + -
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Residues in contact with VAL 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K PRO 4.5 0.9 - - - +
25K ALA 4.4 0.7 - - - -
26K VAL* 1.3 80.2 - - - +
28K SER* 1.3 58.8 + - - +
29K VAL* 4.3 0.7 - - + -
66K SER* 3.3 8.8 - - - -
67K GLY* 2.8 53.7 + - - +
68K VAL 4.4 0.4 - - - +
69K ILE* 3.6 23.1 - - + -
77K VAL* 3.9 17.0 - - + -
92K ILE* 3.9 22.2 - - + -
93K GLN 3.6 9.4 - - - +
94K LEU* 3.6 30.3 - - + -
146K ASN* 5.2 1.3 - - - +
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Residues in contact with SER 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K VAL* 1.3 72.8 - - - +
29K VAL* 1.3 64.9 + - - +
30K ARG* 4.7 3.3 + - - +
64K LEU* 3.7 18.5 - - - +
65K GLY 3.7 4.5 - - - -
91K SER 3.8 0.5 - - - +
92K ILE* 3.3 8.7 - - - +
93K GLN* 2.9 55.0 + - - +
146K ASN* 3.3 23.8 + - - -
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Residues in contact with VAL 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K VAL* 4.3 0.9 - - + -
28K SER* 1.3 77.9 + - - +
30K ARG* 1.3 60.0 - - - +
31K VAL* 4.1 7.8 + - + -
63K GLY 3.8 0.7 - - - +
64K LEU* 3.3 6.8 - - - +
65K GLY 2.9 45.2 + - - +
66K SER 3.6 24.7 - - - +
67K GLY* 3.8 7.9 - - - +
77K VAL* 4.8 0.7 - - + -
79K THR* 4.5 2.9 - - - +
83K VAL* 3.8 10.2 - - + +
84K ILE* 3.7 30.3 - - + -
90K ILE* 4.2 10.1 - - + -
91K SER 3.6 2.2 - - - -
92K ILE* 4.0 17.5 - - + -
116K LEU* 4.5 5.8 - - + -
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Residues in contact with ARG 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K SER* 4.0 4.2 + - - +
29K VAL* 1.3 72.9 - - - +
31K VAL* 1.3 66.8 + - - +
32K GLU* 5.2 8.7 + - + +
62K GLU* 3.2 35.1 + - + +
63K GLY 3.6 7.6 - - - +
64K LEU* 4.4 18.2 - - + +
89K LYS 4.0 0.2 - - - +
90K ILE* 3.4 4.3 - - - +
91K SER* 2.8 57.9 + - - +
93K GLN* 6.5 0.9 - - + -
99K GLU* 6.0 1.2 + - - -
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Residues in contact with VAL 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K VAL* 4.2 7.4 - - + +
30K ARG* 1.3 79.3 - - - +
32K GLU* 1.3 65.7 + - - +
61K PHE* 3.7 24.7 - - + -
62K GLU* 3.3 6.6 - - - +
63K GLY* 2.9 38.9 + - - +
83K VAL* 3.7 26.7 - - + +
84K ILE* 3.9 12.8 - - + -
86K GLN 5.8 0.2 - - - +
87K ALA* 3.7 31.6 - - + +
89K LYS 3.4 2.7 - - - -
90K ILE* 3.9 12.8 - - + -
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Residues in contact with GLU 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 5.2 11.1 + - + +
31K VAL* 1.3 81.4 - - - +
33K GLY* 1.3 54.0 + - - +
61K PHE 3.4 5.8 - - - +
62K GLU* 3.2 34.4 - - + +
87K ALA 3.7 0.2 - - - -
88K GLN* 2.7 30.6 + - - +
89K LYS* 2.9 44.1 + - + +
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Residues in contact with GLY 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K GLU* 1.3 75.1 - - - +
34K THR* 1.3 58.3 + - - -
60K PRO* 3.3 22.9 - - - +
61K PHE* 3.2 26.8 + - - +
86K GLN 3.7 9.6 - - - -
88K GLN* 3.7 20.5 - - - +
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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