Contacts of the strand formed by residues 28 - 37 (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 VAL 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR 3.6 15.5 - - - +
25A ALA* 2.9 14.2 + - - +
26A PRO 4.3 2.3 - - - +
27A ALA* 1.3 80.2 - - - +
29A VAL* 1.3 68.5 + - - +
50A SER* 4.7 1.1 - - - -
51A GLY 3.5 11.7 - - - +
78A LEU* 4.2 14.0 + - - +
110A LEU* 4.8 2.2 - - + -
127A MET* 4.0 30.3 - - + -
128A GLY* 3.7 12.3 - - - +
129A SER* 3.7 31.3 - - - +
130A PRO* 5.4 3.9 - - + +
176A PRO* 4.2 16.2 - - + -
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Residues in contact with VAL 29 (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 5.6 1.3 - - - +
27A ALA 4.2 1.6 - - - +
28A VAL* 1.3 79.4 - - - +
30A TYR* 1.3 63.9 + - - +
31A ILE* 4.2 5.2 - - + -
50A SER* 3.3 6.6 - - - -
51A GLY* 2.9 47.3 + - - +
53A VAL* 4.0 21.8 - - + -
60A ILE* 4.0 18.6 - - + -
75A VAL* 3.9 18.4 - - + -
76A ARG 3.6 9.2 - - - +
77A LEU* 3.6 26.7 - - + -
129A SER* 3.3 11.8 - - - -
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Residues in contact with TYR 30 (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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29A VAL* 1.3 74.9 - - - +
31A ILE* 1.3 61.3 + - - +
32A GLU* 3.2 37.9 + - + -
48A ASN* 2.4 45.3 + - - -
49A GLY 3.6 12.1 - - - -
74A ARG 5.5 0.2 - - - -
75A VAL* 3.0 9.0 - - - +
76A ARG* 2.8 55.7 + - + +
129A SER* 3.3 13.2 + - - +
131A PHE* 3.0 48.0 + - + -
132A ALA* 3.4 9.9 - - + -
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Residues in contact with ILE 31 (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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29A VAL* 4.2 10.1 - - + -
30A TYR* 1.3 78.7 - - - +
32A GLU* 1.3 67.2 + - - +
33A ILE* 5.6 0.9 - - + -
48A ASN* 3.5 5.7 - - - +
49A GLY 3.0 30.7 + - - +
50A SER 3.8 7.6 - - - +
51A GLY* 4.2 6.5 - - - -
60A ILE* 4.4 2.2 - - + -
62A THR* 3.2 41.3 - - + +
66A VAL* 3.6 23.8 - - + +
67A VAL* 4.6 6.3 - - + -
73A VAL* 4.0 24.9 - - + -
74A ARG 3.4 2.5 - - - -
75A VAL* 4.3 7.2 - - + -
99A LEU* 4.1 14.8 - - + -
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Residues in contact with GLU 32 (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* 3.2 35.8 + - + -
31A ILE* 1.3 78.4 - - - +
33A ILE* 1.3 75.7 + - - +
34A LEU* 4.0 28.4 + - + +
36A ARG* 5.1 0.2 + - - -
47A SER 4.0 2.2 - - - +
48A ASN* 3.7 9.7 - - - +
73A VAL* 3.8 1.8 - - - -
74A ARG* 2.8 69.3 + - + +
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Residues in contact with ILE 33 (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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31A ILE* 5.6 2.0 - - + -
32A GLU* 1.3 76.1 - - - +
34A LEU* 1.3 61.0 + - - +
35A ASP* 4.3 1.6 - - - +
45A PRO* 4.3 0.7 - - - +
46A ILE* 3.0 37.9 + - + -
47A SER* 3.1 27.1 + - - +
66A VAL 3.6 20.4 - - - +
67A VAL 3.7 20.6 - - - +
68A ALA* 4.7 1.3 - - + +
70A ARG* 3.0 45.5 - - + +
72A ARG 5.1 2.5 - - - +
73A VAL* 3.7 22.9 - - + +
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Residues in contact with LEU 34 (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* 3.9 30.5 + - + +
33A ILE* 1.3 75.1 - - - +
35A ASP* 1.3 63.3 + - - +
36A ARG* 3.4 31.3 + - - +
43A GLU* 3.2 31.0 - - + +
44A VAL 3.6 25.1 - - - +
45A PRO* 3.7 20.6 - - + -
74A ARG* 5.7 1.8 + - - -
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Residues in contact with ASP 35 (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 1.0 - - - +
34A LEU* 1.3 70.6 - - - +
36A ARG* 1.3 62.4 + - - +
37A HIS* 3.8 24.1 + - + +
43A GLU* 3.3 8.0 - - - +
44A VAL* 2.9 42.3 + - + +
46A ILE* 3.3 18.5 - - + +
70A ARG* 3.1 38.6 + - - -
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Residues in contact with ARG 36 (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* 5.1 0.4 + - - -
34A LEU* 3.4 28.8 + - - +
35A ASP* 1.3 72.0 - - - +
37A HIS* 1.3 69.5 + - - +
38A PRO* 3.3 15.5 - - + +
43A GLU* 2.5 51.0 + - + -
74A ARG* 2.9 46.0 - - - +
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Residues in contact with HIS 37 (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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35A ASP* 3.8 26.2 + - + +
36A ARG* 1.3 79.6 + - - +
38A PRO* 1.3 53.8 - - - +
39A PHE 3.6 1.8 - - - -
40A LEU* 3.5 24.0 + - + +
41A GLY* 2.9 28.1 + - - -
42A ARG* 2.8 36.7 + - + +
43A GLU* 4.4 1.1 - - - +
44A VAL* 3.6 32.0 - - + +
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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