Contacts of the strand formed by residues 42 - 55 (chain A) in PDB entry 1LCY
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 ARG 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A HIS* 2.8 38.6 + - + +
40A LEU* 3.7 39.6 - - + +
41A GLY* 1.3 78.7 - - - +
43A GLU* 1.3 88.8 + - - +
44A VAL* 3.7 20.8 - - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.2 22.4 - - + +
35A ASP 3.3 11.4 - - - +
36A ARG* 2.5 49.7 + - + -
37A HIS* 4.4 1.1 - - - +
42A ARG* 1.3 91.7 - - - +
44A VAL* 1.3 67.8 + - - +
45A PRO* 3.8 8.3 - - + +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 3.7 2.7 - - - -
35A ASP* 2.9 35.3 + - + -
37A HIS* 3.6 27.6 - - + +
42A ARG* 3.7 21.1 - - - +
43A GLU* 1.3 78.5 - - - +
45A PRO* 1.3 73.4 - - + +
46A ILE* 3.1 23.2 + - + +
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Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE 4.3 1.3 - - - +
34A LEU* 3.7 17.3 - - + -
43A GLU* 3.8 8.3 - - + +
44A VAL* 1.3 91.5 - - + +
46A ILE* 1.3 62.3 + - - +
47A SER 5.9 0.2 - - - +
265A LEU* 6.0 2.1 - - - +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.0 35.2 + - + +
35A ASP* 3.3 35.4 - - - +
44A VAL* 3.4 31.0 - - + +
45A PRO* 1.3 75.5 - - - +
47A SER* 1.3 64.3 + - - +
68A ALA* 5.7 4.0 - - + -
70A ARG* 4.0 18.4 - - - +
264A ILE* 5.5 12.5 - - + +
265A LEU 6.1 0.7 - - - +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 4.4 0.7 - - - +
33A ILE* 3.1 40.8 + - - +
46A ILE* 1.3 84.0 + - - +
48A ASN* 1.3 73.4 + - - +
65A HIS* 3.6 7.2 + - - -
66A VAL* 2.5 39.1 + - - -
68A ALA* 5.3 5.2 - - - -
264A ILE* 6.4 1.6 - - - -
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 2.4 46.3 + - - -
31A ILE 3.5 9.0 - - - +
32A GLU* 3.7 8.5 - - - +
47A SER* 1.3 82.8 + - - +
49A GLY* 1.3 58.1 + - - +
65A HIS* 5.7 2.1 + - - -
66A VAL* 4.1 13.2 + - - +
131A PHE 4.6 0.2 + - - -
132A ALA* 4.2 3.6 - - - +
133A LEU 4.6 0.6 - - - +
170A PHE* 3.0 48.2 - - + +
173A ALA* 6.0 0.7 - - - +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 3.6 10.6 - - - -
31A ILE* 3.0 31.2 + - - +
48A ASN* 1.3 78.9 - - - +
50A SER* 1.3 63.9 + - - -
66A VAL* 4.1 9.1 - - - +
132A ALA* 4.3 5.6 - - - -
170A PHE 4.3 12.6 - - - -
173A ALA* 3.9 8.1 - - - -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.7 0.2 - - - -
29A VAL 3.3 7.2 - - - -
31A ILE* 3.8 5.6 - - - +
49A GLY* 1.3 76.6 - - - -
51A GLY* 1.3 59.5 + - - +
62A THR* 2.8 23.3 + - - -
128A GLY* 3.4 7.9 - - - -
129A SER* 2.8 33.7 + - - -
132A ALA* 3.9 2.3 - - - +
171A GLY 3.7 9.5 + - - -
172A ASN* 4.0 1.1 - - - -
173A ALA 2.9 15.5 + - - -
174A GLY* 3.1 10.5 - - - -
175A GLY* 3.8 14.4 - - - -
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.5 7.8 - - - +
29A VAL* 2.9 37.7 + - - +
31A ILE* 4.2 4.3 - - - -
50A SER* 1.3 76.5 - - - +
52A PHE* 1.3 65.9 + - - +
60A ILE* 4.5 0.2 - - - -
61A VAL 3.0 16.4 - - - -
174A GLY 3.3 6.5 - - - -
175A GLY* 4.6 0.9 - - - -
176A PRO* 4.3 1.6 - - - +
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 3.2 13.2 - - - +
28A VAL* 4.3 0.4 - - - +
29A VAL* 4.4 1.6 - - - +
51A GLY* 1.3 76.5 - - - +
53A VAL* 1.3 73.0 + - - +
54A VAL* 3.5 4.9 + - + -
60A ILE* 3.4 7.4 - - - +
61A VAL* 3.0 66.5 + - + -
110A LEU* 4.0 15.3 - - + -
112A LEU* 4.3 12.3 - - + -
174A GLY 3.9 9.4 - - - -
175A GLY 4.2 0.2 - - - -
176A PRO* 3.5 35.9 - - + -
184A VAL* 3.9 37.0 - - + -
187A VAL* 4.2 7.9 - - + -
205A LEU* 3.9 9.2 - - + -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO 5.3 1.3 - - - +
27A ALA* 2.8 23.5 + - - +
29A VAL* 4.0 17.9 - - + -
52A PHE* 1.3 71.7 - - - +
54A VAL* 1.3 59.0 + - - +
55A ALA 3.2 26.7 - - - +
59A LEU 3.6 8.7 - - - +
60A ILE* 4.3 8.5 - - + -
77A LEU* 5.3 2.0 - - + -
107A LEU* 4.0 26.7 - - + -
108A PRO* 3.2 27.4 - - + +
109A THR* 3.5 5.7 - - + -
110A LEU* 3.1 27.9 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.5 5.5 + - + +
53A VAL* 1.3 74.4 - - - +
55A ALA* 1.3 63.7 + - + +
59A LEU* 2.9 41.9 + - + +
61A VAL* 4.1 21.5 - - + -
109A THR* 4.0 10.9 - - - +
110A LEU 4.2 11.0 - - - +
112A LEU* 4.1 26.2 - - + -
209A LEU* 4.0 22.4 - - + -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL* 3.2 12.0 - - - +
54A VAL* 1.3 81.0 - - + +
56A ALA* 1.3 66.4 + - - +
57A ASP* 3.9 14.6 - - - +
58A GLY 3.0 13.5 + - - -
59A LEU* 3.3 33.7 + - + -
100A ARG* 5.1 0.4 - - - +
109A THR* 3.5 4.3 - - - -
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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