Contacts of the strand formed by residues 15 - 21 (chain f) in PDB entry 6FF7
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 TYR 15 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12f HIS* 2.6 30.8 + - + +
13f ILE 4.5 0.4 - - - +
14f ASP* 1.3 76.8 - - - +
16f ARG* 1.3 58.8 + - - +
17f MET* 4.8 2.9 - - + +
30f THR* 3.2 5.4 - - - -
31f PHE* 2.4 43.5 + - + +
84f GLY 5.5 1.6 - - - +
86f PRO* 4.2 11.7 - - + -
87f PRO 5.2 0.7 - - - -
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Residues in contact with ARG 16 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15f TYR* 1.3 71.4 - - - +
17f MET* 1.3 62.9 + - - +
28f ILE* 6.4 0.7 - - + -
29f GLY* 2.9 18.4 - - - +
30f THR* 4.0 2.9 - - - +
82f VAL* 4.6 1.9 - - - +
83f GLU* 4.0 3.3 + - + +
84f GLY* 3.4 29.6 + - - +
85f PRO 4.2 18.9 + - - +
86f PRO* 4.4 1.4 - - - +
87f PRO* 4.6 13.2 - - + +
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Residues in contact with MET 17 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12f HIS* 6.3 2.0 - - + -
15f TYR* 3.5 5.7 + - + -
16f ARG* 1.3 76.6 - - - +
18f ARG* 1.3 63.0 + - - +
19f CYS* 4.1 3.1 - - + +
27f PHE 3.7 1.2 - - - +
28f ILE* 3.5 5.5 - - - +
29f GLY 2.8 29.1 + - - +
31f PHE* 4.1 18.4 - - + -
80f MET* 5.0 11.7 - - + -
81f THR 3.5 9.4 - - - +
82f VAL* 5.0 1.6 - - - +
83f GLU* 4.7 3.6 - - - +
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Residues in contact with ARG 18 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17f MET* 1.3 74.1 - - - +
19f CYS* 1.3 61.4 + - - +
20f ILE* 5.3 0.9 - - - +
26f ILE* 6.2 3.6 - - + -
27f PHE 3.5 5.8 - - - +
28f ILE* 4.6 3.8 - - + +
79f SER 3.7 1.2 - - - +
80f MET* 3.1 6.1 + - - -
81f THR* 2.6 46.0 + - - +
83f GLU* 3.9 19.5 - - + -
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Residues in contact with CYS 19 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17f MET* 5.7 2.5 - - + -
18f ARG* 1.3 74.1 - - - +
20f ILE* 1.3 61.6 + - - +
25f ARG 3.8 0.7 - - - +
26f ILE* 3.4 4.4 - - - +
27f PHE* 2.7 54.1 + - + +
40f LEU* 5.9 6.7 - - + -
77f LEU* 6.4 2.0 - - + -
79f SER 3.3 8.7 - - - +
80f MET* 4.4 5.2 - - + +
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Residues in contact with ILE 20 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18f ARG 5.3 0.9 - - - +
19f CYS* 1.3 77.0 - - - +
21f LEU* 1.3 58.0 + - - +
24f GLY* 6.0 2.2 - - - -
25f ARG 3.5 7.0 - - - +
26f ILE* 5.2 4.9 - - + -
77f LEU* 3.4 4.6 - - - +
78f VAL* 2.5 38.9 + - + -
79f SER* 3.0 24.9 + - - +
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Residues in contact with LEU 21 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20f ILE* 1.3 79.2 - - - +
22f GLN* 1.3 61.5 + - - +
23f ASP* 3.4 9.9 - - + +
24f GLY* 3.7 9.2 + - - -
25f ARG* 3.2 26.1 + - + +
76f ASN* 3.1 20.9 - - + +
77f LEU* 4.3 0.9 - - - +
78f VAL* 3.5 12.0 - - - +
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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
------------------------------------------------------------
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