Contacts of the strand formed by residues 25 - 33 (chain B) in PDB entry 3Q41
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 LYS 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B PRO* 1.3 69.6 - - - +
26B ILE* 1.3 79.4 + - - +
27B VAL* 3.5 5.4 + - + +
57B LYS 3.2 11.5 + - - +
58B ILE* 3.4 24.8 - - + +
59B GLN* 2.9 25.1 + - - -
88B TYR* 3.7 10.3 + - - -
296B LEU* 4.6 11.5 - - + +
303B ASP* 3.3 30.8 + - - -
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PRO 3.3 15.2 + - - +
25B LYS* 1.3 91.1 - - - +
27B VAL* 1.3 62.9 + - - +
28B ASN* 4.2 7.8 + - - +
59B GLN* 3.6 20.4 - - + +
61B ASN* 4.0 25.6 - - + +
88B TYR* 5.0 1.7 - - - -
405B NAG 3.9 31.6 - - + +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS* 3.5 12.1 + - + +
26B ILE* 1.3 76.5 - - - +
28B ASN* 1.3 61.8 + - - +
29B ILE* 3.8 1.5 + - + -
58B ILE* 4.6 5.6 - - + -
59B GLN 3.1 8.9 + - - +
60B LEU* 3.5 27.7 - - + +
61B ASN* 2.9 24.4 + - - -
88B TYR* 3.5 44.4 - - + +
292B VAL* 3.9 17.9 - - + -
296B LEU* 4.1 20.9 - - + -
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Residues in contact with ASN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 4.6 6.6 + - - +
27B VAL* 1.3 73.9 - - - +
29B ILE* 1.3 65.9 + - - +
61B ASN* 2.9 34.4 + - - -
63B THR* 4.4 8.8 - - + +
85B SER* 3.3 21.7 + - - +
86B GLN* 3.1 28.2 + - - +
87B VAL* 4.4 6.5 - - + -
88B TYR* 3.4 29.3 + - - -
405B NAG 3.4 27.0 + - - +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 4.7 2.7 - - + +
28B ASN* 1.3 79.8 - - - +
30B GLY* 1.3 67.1 + - - +
42B PHE* 3.5 27.6 - - + -
46B VAL* 5.0 8.1 - - + -
60B LEU* 3.7 39.9 - - + -
61B ASN 2.8 16.1 + - - +
63B THR* 3.3 25.1 + - - +
88B TYR* 4.9 6.7 - - + -
89B ALA 4.1 9.6 - - - +
91B LEU* 4.5 11.0 - - + -
285B VAL* 5.6 4.7 - - + -
288B VAL* 3.5 31.0 - - + -
289B ALA 4.8 1.1 - - - +
292B VAL* 4.4 4.0 - - + -
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 1.3 79.6 - - - +
31B ALA* 1.3 62.2 + - - +
42B PHE* 4.3 0.9 - - - -
63B THR* 3.2 9.0 - - - -
82B LEU* 4.6 6.3 - - - -
87B VAL* 3.7 21.2 - - - +
89B ALA 3.1 18.2 + - - +
90B ILE* 3.9 7.0 - - - -
91B LEU* 2.9 18.9 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLY* 1.3 76.3 - - - +
32B VAL* 1.3 61.5 + - - +
33B LEU* 3.8 22.0 - - + -
42B PHE* 3.7 25.1 - - + -
63B THR 3.4 5.7 + - - -
64B SER* 3.2 5.9 - - - -
65B VAL 3.1 23.7 + - - -
82B LEU* 4.2 7.5 - - - +
90B ILE* 4.0 0.8 - - - +
91B LEU* 3.2 23.1 - - + +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 1.3 72.3 - - - +
33B LEU* 1.3 55.5 + - - +
65B VAL* 3.3 18.6 - - + +
67B HIS* 3.6 19.1 - - + -
74B MET* 3.6 33.0 - - + -
78B VAL* 5.2 1.3 - - + -
82B LEU* 4.6 4.3 - - + -
90B ILE* 4.1 8.5 - - + +
91B LEU 2.6 17.3 + - - +
92B VAL* 3.7 26.2 - - + -
93B SER* 2.5 37.1 + - - +
107B VAL* 4.0 12.3 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 3.8 24.2 - - + -
32B VAL* 1.3 77.5 - - - +
34B SER* 1.3 61.2 + - - +
35B THR 3.7 1.8 - - - +
38B HIS* 3.6 18.6 - - + +
39B GLU* 3.9 13.7 - - + +
42B PHE* 3.6 30.3 - - + -
64B SER* 4.4 6.7 - - - -
65B VAL 3.2 7.5 + - - +
66B THR* 3.5 5.1 - - - -
67B HIS* 2.7 27.4 + - - +
91B LEU* 4.8 8.3 - - + +
93B SER* 3.8 25.6 - - - -
121B LEU* 4.9 1.8 - - + -
277B GLU* 4.2 3.4 - - - +
281B ILE* 3.9 25.6 - - + -
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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