Contacts of the strand formed by residues 27 - 34 (chain B) in PDB entry 4N41
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 TRP 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG 3.8 0.4 + - - -
26B PRO* 1.3 71.3 - - + +
28B ARG* 1.3 61.7 + - - +
29B LEU* 3.7 13.3 - - + +
65B ALA* 3.4 4.9 - - - -
66B SER 2.9 44.4 + - - +
67B TRP* 3.2 24.0 - - - -
68B SER 3.1 21.8 - - - +
69B PRO* 3.3 32.5 - - + -
70B PRO* 4.1 24.5 - - + +
92B PRO* 6.3 0.7 - - + -
94B GLY* 3.5 14.1 - - - +
95B ARG* 3.1 50.3 - - + +
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Residues in contact with ARG 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 PRO 3.4 0.8 + - - -
27B TRP* 1.3 75.0 - - - +
29B LEU* 1.3 72.9 + - - +
30B GLU* 5.6 5.7 + - - +
60B MET* 3.6 26.2 - - + -
63B GLY* 6.3 0.4 - - - -
64B LEU 3.5 4.3 - - - +
92B PRO* 3.7 1.4 - - - +
93B LYS* 2.9 62.4 + - + +
94B GLY 2.8 14.0 + - - +
95B ARG 5.5 1.2 + - - -
96B ARG* 4.0 35.4 - - + +
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Residues in contact with LEU 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 TRP* 3.7 20.9 - - + +
28B ARG* 1.3 87.6 - - - +
30B GLU* 1.3 64.0 + - - +
57B THR* 6.1 0.4 - - - -
63B GLY* 3.5 4.0 - - - -
64B LEU* 2.9 54.3 + - + +
66B SER* 4.1 12.3 - - - -
70B PRO* 5.1 1.3 - - + -
73B LEU* 3.6 33.4 - - + -
75B LEU* 4.2 3.6 - - + -
90B LEU* 4.2 22.9 - - + -
91B TYR 3.4 5.4 - - - +
92B PRO* 4.0 26.9 - - + -
93B LYS* 5.1 0.4 - - - -
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Residues in contact with GLU 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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28B ARG* 5.6 5.1 + - - +
29B LEU* 1.3 74.1 - - - +
31B VAL* 1.3 70.3 + - - +
32B VAL* 5.0 7.5 - - + +
62B ASP 6.0 0.2 - - - +
63B GLY* 4.9 2.9 - - - -
89B ARG 3.7 0.7 - - - +
90B LEU* 3.3 6.8 - - - +
91B TYR* 2.9 49.0 + - + +
93B LYS* 3.3 31.5 - - + +
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Residues in contact with VAL 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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29B LEU 4.1 2.0 - - - +
30B GLU* 1.3 84.3 - - - +
32B VAL* 1.3 75.7 + - - +
33B LEU* 4.3 17.7 + - + +
46B LEU* 4.5 11.2 - - + -
49B VAL* 4.3 14.8 - - + -
62B ASP 4.1 14.2 + - - +
63B GLY* 4.0 15.9 - - - -
64B LEU* 3.9 27.4 - - + -
88B TYR* 4.9 0.7 - - + -
89B ARG 3.7 1.6 - - - -
90B LEU* 3.9 19.7 - - + -
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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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559A GLU* 3.4 42.2 - - + +
30B GLU* 5.0 9.9 - - - +
31B VAL* 1.3 79.5 - - - +
33B LEU* 1.3 68.0 + - - +
34B ASP 4.3 0.2 + - - -
88B TYR* 3.2 8.0 - - - +
89B ARG* 2.9 54.1 + - + +
91B TYR* 3.9 14.6 - - + -
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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 VAL* 4.2 6.9 + - + -
32B VAL* 1.3 80.3 - - - +
34B ASP* 1.3 61.6 + - - +
35B PRO 3.4 12.4 - - - +
36B PRO* 3.6 10.2 - - - +
37B PRO* 3.9 33.2 - - + -
42B VAL* 4.9 1.3 - - + +
45B LEU* 4.0 14.1 - - + -
46B LEU* 3.8 28.3 - - + -
49B VAL* 4.1 13.2 - - + -
79B LEU* 4.2 11.2 - - + -
86B TYR* 4.5 9.0 - - + -
87B ALA 3.5 5.6 - - - +
88B TYR* 3.7 26.5 - - + -
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Residues in contact with ASP 34 (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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562A ALA 5.3 4.5 - - - +
32B VAL 4.3 0.2 + - - -
33B LEU* 1.3 75.2 - - - +
35B PRO* 1.3 70.4 - - - +
36B PRO* 4.7 4.3 - - - +
85B THR 4.3 0.3 - - - +
86B TYR* 3.4 2.9 - - - -
87B ALA* 2.9 45.9 + - + +
89B ARG* 4.2 29.3 + - - +
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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