Contacts of the strand formed by residues 40 - 49 (chain L) in PDB entry 1H64
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 40 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5K PRO* 4.6 0.4 - - - -
9L ILE* 5.0 5.2 - - + -
19L VAL* 4.2 25.4 - - + -
31L LEU* 4.0 12.6 - - + -
33L GLY 3.6 7.4 - - - +
34L TYR* 4.1 12.8 - - + +
38L LEU* 3.6 13.2 + - - +
39L ASN* 1.3 80.1 - - - +
41L VAL* 1.3 64.7 + - - +
42L LEU* 4.2 5.2 - - + -
60L ILE 3.8 0.3 - - - +
61L VAL* 3.3 5.4 - - - +
62L ILE* 2.8 55.0 + - + +
67L VAL* 5.9 1.3 - - + -
70L ILE* 4.0 20.0 - - + -
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Residues in contact with VAL 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K GLU 3.4 22.2 - - - +
4K ARG 3.9 0.7 - - - -
5K PRO* 3.7 30.3 - - + -
8K VAL* 3.7 21.1 - - + -
31L LEU* 3.6 6.8 - - - +
32L ILE* 3.0 50.2 + - + -
33L GLY 3.0 9.6 + - - +
40L VAL* 1.3 78.5 - - - +
42L LEU* 1.3 63.4 + - - +
59L LYS* 4.0 11.2 - - + -
60L ILE 3.3 6.1 - - - +
61L VAL* 4.1 6.1 - - + -
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Residues in contact with LEU 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L VAL* 3.7 26.0 - - + -
19L VAL* 4.0 13.5 - - + -
27L PHE* 4.0 10.5 - - + -
28L ARG* 4.0 7.0 - - - -
29L GLY* 3.9 21.8 - - - +
30L ARG 3.2 10.1 - - - +
31L LEU* 4.0 9.6 - - + -
32L ILE* 4.5 3.4 - - - -
40L VAL* 4.5 3.8 - - + -
41L VAL* 1.3 81.1 - - - +
43L ALA* 1.3 60.6 + - - +
45L ALA* 3.8 15.8 - - + +
59L LYS* 3.3 6.4 - - - +
60L ILE* 2.9 35.8 + - + +
62L ILE* 3.7 30.7 - - + -
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Residues in contact with ALA 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L GLY* 3.8 0.5 - - - -
30L ARG* 2.9 62.9 + - - +
32L ILE* 3.7 19.1 - - + -
42L LEU* 1.3 71.9 - - - +
44L ASP* 1.3 76.1 + - - +
45L ALA 3.2 2.8 + - - -
58L GLY 3.3 8.3 - - - +
59L LYS* 4.4 3.6 - - + +
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Residues in contact with ASP 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L ARG 4.2 0.3 - - - +
29L GLY* 4.0 7.1 - - - -
30L ARG* 4.1 17.7 + - + +
43L ALA* 1.3 78.0 - - - +
45L ALA* 1.3 61.3 + - - +
46L GLU* 5.3 3.1 - - - +
57L TYR 3.4 7.9 - - - -
58L GLY* 2.7 25.1 + - - +
56V ARG* 4.5 7.7 + - - -
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Residues in contact with ALA 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L PHE* 5.5 1.3 - - + -
28L ARG 3.1 13.2 - - - +
42L LEU* 3.8 19.3 - - + +
43L ALA 3.9 2.0 - - - +
44L ASP* 1.3 78.4 - - - +
46L GLU* 1.3 65.4 + - - +
56L ARG* 3.3 7.8 - - - +
57L TYR* 2.8 35.7 + - + +
60L ILE* 3.8 29.4 - - + +
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Residues in contact with GLU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L PHE* 3.2 10.0 - - - -
28L ARG* 2.9 63.6 + - + +
44L ASP 5.3 2.9 - - - +
45L ALA* 1.3 78.5 - - - +
47L MET* 1.3 60.8 + - - +
48L ILE* 3.8 19.2 + - + +
53L VAL* 3.8 24.7 - - + +
55L LYS 3.1 11.2 - - - +
56L ARG* 3.7 25.0 + - + +
57L TYR* 4.4 0.9 - - - -
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Residues in contact with MET 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ILE* 4.3 16.4 - - + -
26K GLU* 5.6 1.8 - - - +
25L PHE* 3.2 46.4 - - + -
26L GLU 3.4 7.0 - - - +
27L PHE* 3.6 22.2 - - + -
46L GLU* 1.3 72.9 - - - +
48L ILE* 1.3 60.9 + - - +
49L GLN* 6.4 0.2 - - - -
53L VAL* 3.5 4.7 - - - -
54L VAL* 2.8 47.6 + - + -
55L LYS* 2.8 13.5 + - + +
57L TYR* 3.2 35.2 - - + +
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Residues in contact with ILE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L GLY 4.3 0.5 - - - +
25L PHE* 3.6 6.6 - - - -
26L GLU* 2.6 54.2 + - + +
28L ARG* 3.2 58.6 - - + +
46L GLU* 3.9 19.1 - - + +
47L MET* 1.3 81.0 - - - +
49L GLN* 1.3 63.3 + - - +
51L GLY* 3.6 36.3 - - - +
52L GLU 3.4 3.4 - - - +
53L VAL* 4.5 9.4 - - + -
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Residues in contact with GLN 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L GLY 4.1 8.1 - - - +
25L PHE* 4.8 13.2 - - + -
48L ILE* 1.3 75.3 - - - +
50L ASP* 1.4 81.2 + - + +
51L GLY 3.1 1.1 - - - -
52L GLU* 2.9 22.1 + - - +
54L VAL* 4.1 26.1 - - + +
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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