Contacts of the helix formed by residues 2 - 14 (chain L) in PDB entry 5WFE
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 THR 2 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52I T 3.2 51.4 + - - +
53I T 3.0 16.3 + - - -
45K LYS* 3.3 30.5 - - + +
46K LEU* 4.3 3.1 - - - +
47K SER* 5.9 1.1 - - - -
1L MET* 1.3 78.4 - - - +
3L LYS* 1.3 67.8 + - - +
4L SER 3.5 0.2 - - - -
5L GLU* 3.4 20.6 + - - +
6L LEU* 3.0 21.8 + - - +
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Residues in contact with LYS 3 (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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52I T 5.0 0.2 - - - +
53I T 3.0 20.6 + - - +
54I T 4.5 4.0 + - - +
45K LYS 4.1 3.6 + - - -
46K LEU* 4.2 12.7 - - + +
47K SER* 4.5 24.7 + - - +
2L THR* 1.3 78.3 - - - +
4L SER* 1.3 63.6 + - - +
6L LEU* 3.1 15.7 + - - +
7L ILE* 3.2 23.7 + - + +
26L VAL* 4.7 12.2 - - + +
27L LYS* 3.6 56.2 + - - +
30L LEU* 5.2 12.1 - - + -
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Residues in contact with SER 4 (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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53I T 2.4 56.6 + - - -
54I T 5.8 6.3 - - - -
2L THR* 4.1 0.9 + - - -
3L LYS* 1.3 68.7 - - - +
5L GLU* 1.3 64.4 + - - +
7L ILE* 2.9 36.1 + - - +
8L GLU* 3.3 14.5 + - - +
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Residues in contact with GLU 5 (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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52I T 5.4 3.1 + - - -
53I T 5.3 0.4 - - - +
42K GLU* 4.7 1.6 - - - +
1L MET* 3.2 36.6 + - + +
2L THR* 3.4 18.7 + - - +
3L LYS 3.3 0.8 - - - -
4L SER* 1.3 87.0 + - - +
6L LEU* 1.3 61.4 + - - +
7L ILE 3.5 0.2 + - - -
8L GLU* 3.8 8.3 + - - +
9L ARG* 3.5 35.1 + - - +
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Residues in contact with LEU 6 (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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30K PHE* 3.8 28.7 - - + +
33K GLU* 3.7 26.2 - - + -
34K ILE* 4.1 21.8 - - + -
44K VAL* 5.7 0.4 - - + -
46K LEU* 4.5 15.3 - - + -
1L MET* 3.5 28.8 - - + +
2L THR 3.0 14.4 + - - +
3L LYS* 3.3 10.1 - - - +
5L GLU* 1.3 75.9 - - - +
7L ILE* 1.3 64.8 + - - +
9L ARG* 3.6 2.8 + - - +
10L LEU* 3.3 29.0 + - + +
26L VAL* 4.5 8.1 - - + -
30L LEU* 5.7 0.4 - - + -
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Residues in contact with ILE 7 (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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54I T 6.1 0.7 - - - +
3L LYS* 3.3 20.6 - - + +
4L SER* 2.9 25.8 + - - +
6L LEU* 1.3 77.3 - - - +
8L GLU* 1.3 67.3 + - + +
10L LEU* 3.1 9.2 + - - +
11L ALA* 3.0 19.6 + - + +
19L ALA* 4.8 2.5 - - + +
22L VAL* 3.6 23.3 - - + +
23L GLU* 3.8 42.6 - - + +
26L VAL* 4.2 19.3 - - + -
27L LYS* 5.2 6.7 - - - +
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Residues in contact with GLU 8 (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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4L SER* 3.3 14.5 + - - +
5L GLU* 3.8 7.2 + - - +
6L LEU 3.4 0.2 - - - -
7L ILE* 1.3 80.3 - - + +
9L ARG* 1.3 54.3 + - + +
11L ALA* 3.1 7.9 + - - +
12L THR* 2.6 42.2 + - - +
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Residues in contact with ARG 9 (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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33K GLU* 3.8 26.7 + - + +
37K ALA* 4.9 4.4 - - - +
40K ASN* 6.1 0.8 - - - +
42K GLU* 3.6 28.3 + - - -
1L MET* 3.1 37.1 - - - +
5L GLU* 3.5 17.0 + - - +
6L LEU 3.6 6.7 + - - +
7L ILE 3.3 0.6 - - - -
8L GLU* 1.3 76.9 - - + +
10L LEU* 1.3 61.3 + - - +
12L THR* 3.4 9.1 - - - -
13L GLN* 3.1 31.3 + - - +
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Residues in contact with LEU 10 (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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26K LEU* 5.5 8.5 - - + +
29K LEU* 3.8 35.2 - - + +
30K PHE* 4.1 19.3 - - + +
33K GLU* 3.8 17.7 - - + -
6L LEU* 3.3 20.1 + - + +
7L ILE 3.1 6.7 + - - +
8L GLU 3.1 0.6 - - - -
9L ARG* 1.3 75.3 - - - +
11L ALA* 1.3 54.0 + - - +
13L GLN* 3.0 13.2 + - - +
14L GLN* 2.7 41.3 + - + +
22L VAL* 3.9 13.5 - - + -
26L VAL* 3.8 27.8 - - + -
29L MET* 5.5 1.6 - - + -
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Residues in contact with ALA 11 (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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7L ILE* 3.0 13.8 + - + +
8L GLU* 3.6 9.9 - - - +
10L LEU* 1.3 75.2 - - - +
12L THR* 1.3 63.7 + - - +
14L GLN 3.0 27.1 - - - +
15L SER* 3.5 3.5 + - - -
17L ILE 5.2 1.1 - - - +
19L ALA* 4.2 23.8 - - + +
22L VAL* 4.2 20.7 - - + +
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Residues in contact with THR 12 (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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8L GLU* 2.6 31.2 + - - +
9L ARG* 3.4 11.5 - - - +
11L ALA* 1.3 74.2 - - - +
13L GLN* 1.3 64.9 + - + +
15L SER* 4.0 9.0 + - - -
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Residues in contact with GLN 13 (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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29K LEU* 4.6 17.9 - - + +
32K GLU* 6.0 0.9 - - - +
33K GLU* 2.8 30.2 + - - +
36K ARG* 2.9 26.8 + - - +
9L ARG* 3.1 12.9 + - - +
10L LEU* 3.0 16.2 + - - +
12L THR* 1.3 81.7 - - + +
14L GLN* 1.3 72.2 + - + +
15L SER* 3.5 4.6 + - - -
16L HIS* 5.5 1.0 - - - -
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Residues in contact with GLN 14 (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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25K GLU* 3.0 27.4 + - - +
26K LEU* 4.9 7.6 - - + -
29K LEU* 3.2 26.2 - - + +
10L LEU* 2.7 25.9 + - + +
11L ALA* 3.0 13.6 - - - +
13L GLN* 1.3 83.9 + - + +
15L SER* 1.3 64.2 + - - +
16L HIS* 2.5 40.9 + - - -
17L ILE* 3.1 41.9 + - + +
22L VAL* 5.1 2.0 - - + -
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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