Contacts of the helix formed by residues 5 - 17 (chain S) in PDB entry 1XFV
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 5 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3S GLN 3.0 6.3 + - - -
4S LEU* 1.3 72.4 - - - +
6S GLU* 1.3 62.1 + - - +
7S GLU* 3.6 17.4 + - + +
8S GLN* 2.5 71.0 + - + +
9S ILE* 2.9 5.9 + - - +
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Residues in contact with GLU 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672E ARG* 3.6 39.9 + - - +
4S LEU 3.7 1.8 + - - -
5S THR* 1.3 73.1 + - - +
7S GLU* 1.3 70.4 + - + +
9S ILE* 2.5 41.1 + - - +
10S ALA* 3.0 8.1 + - - +
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Residues in contact with GLU 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E SER* 4.3 1.0 + - - +
669E SER* 6.5 0.7 - - - -
672E ARG* 6.4 0.7 - - - -
5S THR* 3.1 15.8 + - + +
6S GLU* 1.3 87.6 - - + +
8S GLN* 1.3 66.3 + - - +
9S ILE 2.9 5.9 + - - -
10S ALA* 3.4 12.3 + - - +
11S GLU* 3.3 42.7 + - + +
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Residues in contact with GLN 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S GLN 4.3 0.7 - - - +
4S LEU* 3.0 18.0 - - + +
5S THR* 2.5 49.1 + - + +
7S GLU* 1.3 81.1 + - - +
9S ILE* 1.3 57.4 + - - +
11S GLU* 4.3 10.3 - - - +
12S PHE* 3.5 35.4 - - + -
76S MET* 2.8 35.9 - - - +
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Residues in contact with ILE 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S LEU* 3.6 31.4 - - + +
5S THR 2.9 11.8 + - - +
6S GLU* 2.5 26.9 + - - +
8S GLN* 1.3 73.3 - - - +
10S ALA* 1.3 57.4 + - - +
11S GLU 2.8 4.0 - - - -
12S PHE* 2.6 26.3 + - - +
13S LYS* 3.1 17.9 + - + +
69S LEU* 3.1 49.4 - - + -
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Residues in contact with ALA 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668E SER* 3.1 21.0 + - - +
671E ARG* 5.3 5.6 - - + +
672E ARG* 5.2 14.8 - - + +
6S GLU* 3.0 6.2 + - - +
7S GLU* 3.9 8.3 - - - +
9S ILE* 1.3 81.0 - - - +
11S GLU* 1.3 56.8 + - - +
13S LYS* 3.8 6.1 - - - +
14S GLU* 2.9 33.0 + - + +
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Residues in contact with GLU 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664E ILE* 4.3 3.5 - - + +
665E LYS* 3.0 46.8 - - + +
668E SER* 3.0 25.2 + - - +
7S GLU* 3.3 40.8 - - + +
8S GLN* 4.5 5.5 - - - +
9S ILE 2.7 1.6 + - - -
10S ALA* 1.3 74.4 - - - +
12S PHE* 1.3 78.7 + - + +
13S LYS 3.0 6.0 + - - -
14S GLU* 3.4 1.9 + - - +
15S ALA* 3.1 24.3 + - - +
39S LEU* 4.5 5.6 - - + +
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Residues in contact with PHE 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S LEU* 5.8 3.1 - - + -
8S GLN* 3.5 32.8 - - + +
9S ILE* 2.6 13.7 + - + +
11S GLU* 1.3 84.6 - - + +
13S LYS* 1.3 59.3 + - - +
15S ALA* 4.5 1.5 - - - +
16S PHE* 2.8 28.1 + - - +
39S LEU* 3.3 31.0 - - + -
41S GLN* 5.5 2.5 - - - -
68S PHE* 3.6 19.9 - + + -
69S LEU* 4.4 16.4 - - + -
72S MET* 3.3 53.4 - - + -
76S MET* 4.5 17.9 - - + -
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Residues in contact with LYS 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671E ARG* 6.3 1.3 - - - +
9S ILE* 3.1 20.2 + - + +
10S ALA* 3.9 9.0 - - - +
11S GLU 3.0 0.2 - - - -
12S PHE* 1.3 86.3 - - - +
14S GLU* 1.3 54.9 + - - +
15S ALA 2.7 15.7 + - - -
16S PHE* 3.9 10.1 - - + -
17S SER* 2.7 35.9 + - - +
65S PHE* 2.7 57.7 + - + +
66S PRO* 3.9 1.6 - - - +
68S PHE* 4.6 4.0 - - - -
69S LEU* 4.2 27.1 - - + +
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Residues in contact with GLU 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664E ILE* 4.1 11.5 - - + +
667E LEU* 3.1 37.3 - - - +
668E SER* 3.3 31.0 - - - +
671E ARG* 3.0 51.6 + - - +
678E VAL* 4.0 5.3 - - - +
679E TYR* 4.3 13.2 + - - -
745E TYR* 4.9 0.2 + - - -
10S ALA 2.9 16.0 + - - +
11S GLU 4.0 2.9 - - - +
13S LYS* 1.3 75.9 - - - +
15S ALA* 1.3 56.7 + - - +
17S SER* 5.1 1.6 - - - -
18S LEU* 3.2 23.9 + - - +
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Residues in contact with ALA 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664E ILE* 3.7 24.9 - - + -
11S GLU 3.1 15.4 + - - +
12S PHE* 4.5 1.8 - - - +
13S LYS 2.8 1.2 - - - -
14S GLU* 1.3 79.3 - - - +
16S PHE* 1.3 66.3 + - - +
17S SER 3.1 2.1 + - - -
18S LEU* 3.3 10.6 + - - -
19S PHE* 3.4 18.2 - - - +
35S VAL* 3.5 14.0 - - + +
38S SER* 4.5 0.9 - - - +
39S LEU* 3.8 21.8 - - + -
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Residues in contact with PHE 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S PHE 2.8 25.2 + - - +
13S LYS* 3.0 10.3 + - - +
15S ALA* 1.3 79.0 - - - +
17S SER* 1.3 66.2 - - - +
19S PHE 3.7 6.4 + - - -
20S ASP* 3.8 9.4 + - - +
25S GLY 3.7 18.6 - - - -
27S ILE* 3.1 59.1 - - + +
35S VAL* 3.5 12.3 - - + +
63S ILE 3.4 4.9 - - - -
64S ASP 3.2 30.7 - - - -
65S PHE* 3.7 27.1 - + + -
68S PHE* 3.7 26.0 - + + -
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Residues in contact with SER 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671E ARG* 5.9 3.1 - - - -
679E TYR* 3.6 13.5 - - - -
691E LYS* 3.7 11.3 + - - -
13S LYS* 2.7 25.4 + - - +
14S GLU* 5.0 1.1 - - - -
16S PHE* 1.3 80.0 - - - +
18S LEU* 1.3 54.6 + - - -
19S PHE 2.7 16.6 + - - -
20S ASP* 2.9 20.0 + - - +
65S PHE* 4.6 12.5 - - - -
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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