Contacts of the strand formed by residues 4 - 14 (chain H) in PDB entry 5FLM
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 ILE 4 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2H ALA* 3.3 19.8 - - + +
3H GLY* 1.3 75.5 - - - +
5H LEU* 1.3 65.0 + - - +
6H PHE 3.9 4.0 - - - +
7H GLU* 3.3 44.6 - - + +
59H VAL* 3.8 15.0 - - + -
60H ILE 4.0 2.2 - - - +
61H ALA* 4.3 6.1 - - + -
66H GLU* 4.3 28.0 - - + +
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Residues in contact with LEU 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLY* 3.7 4.0 + - - +
4H ILE* 1.3 75.9 - - - +
6H PHE* 1.3 60.9 + - - +
60H ILE* 2.9 16.0 + - + +
62H SER* 3.2 34.1 - - - +
131H ASN 4.5 12.0 - - - +
134H GLY* 3.8 29.3 - - - +
135H PHE* 3.5 39.8 - - + -
139H SER* 6.1 0.9 - - - +
140H ARG 5.6 0.2 - - - +
141H VAL* 4.6 10.3 - - + -
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Residues in contact with PHE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ILE* 3.5 1.0 - - - -
5H LEU* 1.3 80.7 - - - +
7H GLU* 1.3 74.2 + - - +
8H ASP* 3.4 30.3 - - + -
10H PHE* 3.5 31.6 - + - -
35H PHE* 5.5 3.4 - + - -
37H MET* 3.4 36.3 - - + -
58H LEU* 4.4 8.3 - - + -
59H VAL* 3.3 1.6 - - - +
60H ILE* 2.9 58.0 + - + +
125H LEU* 4.2 15.9 - - + -
131H ASN* 4.9 12.3 - - + -
132H LEU* 5.1 4.0 - - + -
135H PHE* 4.5 6.3 - - + -
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Residues in contact with GLU 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ILE* 3.3 37.9 - - + +
6H PHE* 1.3 86.1 - - - +
8H ASP* 1.3 66.3 + - - +
35H PHE* 4.4 13.2 - - - -
57H ARG* 5.7 3.8 + - + -
58H LEU 3.4 5.8 - - - +
59H VAL* 3.8 18.9 - - + +
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Residues in contact with ASP 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H PHE* 3.4 24.0 - - + -
7H GLU* 1.3 75.5 - - - +
9H ILE* 1.3 92.1 + - - +
10H PHE* 3.2 13.4 - - + -
32H SER* 2.2 31.9 + - - -
33H GLU* 3.6 9.3 - - - +
34H SER* 4.9 2.3 - - - -
35H PHE* 3.8 23.0 - - + +
37H MET* 4.9 0.7 - - - +
57H ARG* 3.8 3.9 - - - +
58H LEU* 2.9 35.9 + - - +
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ASP* 1.3 93.2 + - - +
10H PHE* 1.3 76.6 + - - +
11H ASP* 5.0 1.3 - - - +
32H SER* 3.6 5.7 + - - -
33H GLU* 3.8 24.3 + - + +
55H LYS* 4.4 15.3 - - + -
56H PHE 3.7 5.4 - - - +
57H ARG* 4.2 17.9 - - + -
148H LEU* 3.9 32.1 - - + -
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Residues in contact with PHE 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H PHE* 3.5 26.0 - + - -
8H ASP* 3.2 25.8 - - + -
9H ILE* 1.3 83.9 - - - +
11H ASP* 1.3 72.8 + - - +
30H CYS* 4.1 6.1 - - + -
31H GLU 3.6 4.7 - - - +
32H SER* 3.4 19.7 - - - -
37H MET* 4.0 12.1 - - + -
39H LEU* 3.4 33.0 - - + -
54H ASP 3.3 0.5 - - - +
55H LYS* 3.1 1.9 - - - -
56H PHE* 2.9 55.8 + + + +
58H LEU* 3.4 32.5 - - + -
125H LEU* 4.3 5.2 - - + -
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Residues in contact with ASP 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 5.0 2.4 - - - +
10H PHE* 1.3 83.1 + - - +
12H VAL* 1.3 65.6 + - - +
13H LYS* 3.5 7.0 + - + +
30H CYS* 2.9 7.2 - - - -
31H GLU* 2.9 40.2 + - + +
33H GLU* 4.4 21.6 + - - +
53H GLY* 6.0 1.8 - - - -
54H ASP 3.3 7.2 - - - +
55H LYS* 3.1 30.4 - - - +
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 1.3 71.0 - - - +
13H LYS* 1.3 62.0 + - - +
14H ASP 3.3 26.9 - - - +
15H ILE* 4.3 6.3 - - + -
28H LEU* 3.7 17.9 - - + -
29H HIS 3.8 4.5 - - - +
30H CYS* 3.6 6.3 - - - -
50H VAL* 4.1 16.8 - - + -
51H ASP 4.1 16.6 - - - +
52H LEU* 4.0 2.8 - - + +
53H GLY* 3.1 23.6 + - - +
54H ASP* 3.4 11.5 + - + +
56H PHE* 3.5 32.8 - - + -
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Residues in contact with LYS 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 3.5 8.9 + - + +
12H VAL* 1.3 74.6 - - - +
14H ASP* 1.3 75.5 + - - +
29H HIS* 2.9 11.3 + - + +
31H GLU* 3.6 41.3 - - + +
36H LYS* 4.2 8.7 - - - +
52H LEU* 3.2 16.5 - - - +
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Residues in contact with ASP 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H VAL* 3.3 13.2 - - - +
13H LYS* 1.3 91.9 - - - +
15H ILE* 1.3 64.8 + - - +
17H PRO* 4.5 17.4 - - + +
27H ARG 4.3 0.2 - - - -
28H LEU* 3.7 1.0 - - - -
29H HIS* 3.2 47.0 + - + +
52H LEU* 3.9 2.9 - - - +
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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