Contacts of the strand formed by residues 27 - 42 (chain B) in PDB entry 1YI5
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 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.9 16.6 - - + -
20B PRO* 3.0 37.7 - - + +
21B THR* 4.9 2.0 - - - -
22B GLN* 5.9 0.4 - - - -
26B PRO* 1.3 74.7 - - - +
28B ALA* 1.3 61.4 + - - +
29B VAL* 3.0 20.0 + - + +
58B TRP* 4.2 25.6 - - + -
59B SER* 4.0 21.1 - - - +
82B TRP* 4.6 7.2 - - + -
149B GLU 3.0 15.8 + - - +
150B ILE* 3.8 5.0 - - + -
151B SER 3.2 18.3 + - - -
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Residues in contact with ALA 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* 3.8 4.4 + - - +
27B VAL* 1.3 71.3 - - - +
29B VAL* 1.3 61.8 + - - +
30B SER* 3.9 2.6 + - - -
57B THR 3.8 0.2 - - - +
58B TRP* 3.5 22.3 - - - +
59B SER* 3.9 17.1 + - - +
151B SER* 4.0 11.4 - - - +
153B ASP* 5.7 0.2 - - - -
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.0 21.6 + - + +
28B ALA* 1.3 74.7 - - - +
30B SER* 1.3 62.3 + - - +
31B VAL* 3.5 22.9 - - + -
56B THR* 4.2 14.1 - - + -
57B THR 3.4 9.2 - - - +
58B TRP* 4.1 12.3 - - + -
82B TRP* 4.8 4.7 - - + -
84B PRO* 4.5 14.1 - - + -
86B LEU* 4.5 7.2 - - + -
150B ILE* 4.0 17.0 - - + -
151B SER 3.0 21.6 + - - +
152B VAL* 3.5 3.8 - - + -
153B ASP* 3.2 21.1 + - - +
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Residues in contact with SER 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 ALA 3.9 3.0 + - - -
29B VAL* 1.3 71.0 - - - +
31B VAL* 1.3 61.2 + - - +
55B GLN* 3.6 5.2 + - - +
57B THR* 3.0 59.6 + - - +
153B ASP* 3.6 6.1 - - - -
155B THR* 4.0 17.9 - - - -
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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
----------------------------------------------------------
29B VAL* 3.5 23.3 - - + -
30B SER* 1.3 78.1 - - - +
32B SER* 1.3 83.8 + - - +
33B LEU* 4.8 2.2 - - + -
54B GLN* 4.8 5.4 - - + -
55B GLN* 3.4 8.5 - - - +
56B THR* 4.4 8.5 - - + +
86B LEU* 4.1 17.9 - - + -
140B ILE* 4.7 21.1 - - + -
152B VAL* 4.5 17.5 - - + -
153B ASP 3.2 7.0 + - - +
154B PRO* 3.5 14.8 - - - +
155B THR 4.2 3.1 + - - -
178B GLN* 3.5 9.4 - - - +
195B VAL* 4.8 15.0 - - + -
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Residues in contact with SER 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 VAL* 1.3 80.4 - - - +
33B LEU* 1.3 72.3 + - - +
34B LYS* 4.0 16.9 - - - -
54B GLN 3.4 3.3 - - - -
55B GLN* 2.8 60.7 + - - +
155B THR 6.0 0.7 - - - -
156B THR* 5.5 0.7 + - - -
161B ASP* 5.3 0.3 + - - -
178B GLN* 3.2 19.3 + - - +
31F SER* 5.8 0.2 - - - -
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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* 4.8 5.6 - - + -
32B SER* 1.3 83.2 + - - +
34B LYS* 1.3 60.3 + - - +
35B PHE* 3.6 38.1 + - + -
52B PHE* 3.8 29.2 - - + -
53B TRP 3.8 2.2 - - - -
54B GLN* 3.5 30.7 - - + +
138B ILE* 4.5 19.1 - - + -
140B ILE* 4.7 11.0 - - + -
161B ASP* 4.3 8.7 - - - +
176B VAL* 4.7 2.1 - - - +
178B GLN* 2.8 21.5 + - - +
197B VAL* 4.0 20.6 - - + +
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Residues in contact with LYS 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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32B SER* 4.0 15.2 - - - +
33B LEU* 1.3 71.2 - - - +
35B PHE* 1.3 63.8 + - - +
36B ILE* 3.5 5.6 + - + +
52B PHE* 3.4 2.2 - - - -
53B TRP* 3.0 42.8 + - + +
55B GLN* 3.7 20.4 - - + +
114B MET* 4.5 4.3 - - + -
156B THR* 5.6 0.6 - - - +
159B SER* 3.4 30.5 + - - -
161B ASP* 3.5 29.6 + - + +
26F CYS* 6.2 0.6 - - - -
27F ASP 4.6 9.7 + - - -
28F ALA* 4.0 32.7 + - + +
30F CYS* 5.9 0.4 - - - +
31F SER* 3.6 23.1 + - - +
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.6 40.4 + - + -
34B LYS* 1.3 69.6 - - - +
36B ILE* 1.3 62.3 + - - +
38B ILE* 5.2 1.6 - - + -
50B VAL* 3.7 29.2 - - + -
52B PHE* 4.0 8.5 - + + -
138B ILE* 4.1 24.7 - - + -
161B ASP* 4.7 10.7 + - + +
165B PHE* 3.3 24.6 + - + +
173B ILE* 3.8 19.8 - - + +
176B VAL* 4.4 7.9 - - + -
197B VAL* 3.8 19.1 - - + -
199B LEU* 3.3 48.0 - - + -
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Residues in contact with ILE 36 (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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89A TYR 5.4 5.4 - - - +
90A ASN* 6.3 1.6 - - - -
91A ALA 6.2 0.2 - - - +
34B LYS* 3.5 17.7 - - + +
35B PHE* 1.3 71.7 - - - +
37B ASN* 1.3 65.5 + - + +
51B VAL* 2.9 26.2 + - + +
52B PHE* 3.7 2.2 - - - +
53B TRP* 3.2 62.8 - - + +
164B TYR* 4.8 19.5 - - + -
165B PHE* 2.8 21.6 - - - +
166B SER* 2.9 21.9 + - - +
28F ALA* 5.2 4.0 - - + -
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Residues in contact with ASN 37 (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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92A ILE* 6.1 1.3 - - + -
122A SER* 2.8 32.3 + - - -
36B ILE* 1.3 87.4 - - + +
38B ILE* 1.3 84.9 + - - +
39B LEU* 3.7 13.6 + - + +
50B VAL* 3.6 3.1 - - - +
51B VAL* 3.0 36.9 + - + +
165B PHE* 3.4 5.0 - - - -
166B SER* 3.3 26.5 + - - -
169B SER* 3.4 15.3 - - - +
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Residues in contact with ILE 38 (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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35B PHE* 5.2 1.3 - - + -
37B ASN* 1.3 81.5 + - - +
39B LEU* 1.3 61.7 + - - +
41B VAL* 3.9 18.2 - - + -
48B VAL* 4.7 6.7 - - + -
49B ASP 3.9 6.7 - - - +
50B VAL* 4.2 14.1 - - + -
165B PHE* 3.6 27.6 - - + -
169B SER* 2.9 18.8 + - - +
170B ARG 4.6 1.2 + - - -
171B PHE* 3.5 30.9 - - + -
173B ILE* 4.5 5.2 - - + -
199B LEU* 4.0 11.9 - - + -
201B PHE* 3.8 41.7 - - + -
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Residues in contact with LEU 39 (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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45A THR* 5.5 5.1 - - - +
47A GLU* 3.5 30.1 - - + +
92A ILE* 4.5 22.7 - - + -
122A SER* 4.9 1.3 - - - +
37B ASN* 4.1 24.9 - - + +
38B ILE* 1.3 75.9 - - - +
40B GLU* 1.3 62.4 + - + +
41B VAL 4.1 0.2 + - - -
49B ASP* 2.8 21.4 + - + +
51B VAL* 3.8 14.1 - - + -
118B ARG* 3.4 44.4 - - - +
170B ARG* 4.6 10.9 + - - +
171B PHE* 3.9 11.2 - - - -
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Residues in contact with GLU 40 (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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39B LEU* 1.3 77.1 - - + +
41B VAL* 1.3 73.1 + - - +
42B ASN* 5.1 9.9 + - - +
47B GLU 4.5 0.9 - - - -
48B VAL* 3.5 1.4 - - - -
49B ASP* 2.9 48.8 + - + +
118B ARG* 5.7 1.2 + - - -
120B ARG* 2.8 34.2 + - - +
170B ARG* 5.6 2.0 - - - +
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Residues in contact with VAL 41 (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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38B ILE* 3.9 15.3 - - + -
39B LEU 4.1 1.0 + - - -
40B GLU* 1.3 85.6 - - - +
42B ASN* 1.3 66.6 - - - +
43B GLU 4.0 1.3 + - - +
47B GLU 3.6 6.3 - - - +
48B VAL* 4.3 11.0 - - + -
125B VAL* 3.4 28.5 - - + -
128B VAL* 4.1 12.8 - - + -
170B ARG* 4.6 13.6 + - - +
171B PHE* 3.2 39.4 - - + -
201B PHE* 4.5 5.4 - - + -
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Residues in contact with ASN 42 (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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40B GLU* 5.1 10.9 + - - +
41B VAL* 1.3 75.4 - - - +
43B GLU* 1.3 66.6 + - - +
44B ILE* 3.0 27.1 + - - +
45B THR* 3.0 28.4 + - - +
46B ASN* 2.9 19.8 + - - -
47B GLU* 3.1 20.5 + - + +
120B ARG* 5.3 0.2 - - - +
125B VAL* 4.2 2.7 - - - -
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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
------------------------------------------------------------
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