Contacts of the strand formed by residues 41 - 46 (chain h) 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 GLN 41 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3339 ILE* 4.8 8.5 - - + -
35h SER* 5.5 1.0 - - - -
39h ASN 4.3 0.2 + - - -
40h THR* 1.3 80.4 - - - +
42h VAL* 1.3 61.6 + - - +
54h GLY 3.2 15.0 - - - +
55h ARG* 4.7 0.9 - - - +
110h LEU 4.5 1.4 - - - +
111h ARG* 4.7 7.8 - - - +
112h ASN 4.8 3.3 + - - +
114h LEU* 4.3 17.0 - - + +
115h ILE* 3.5 27.4 + - + +
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Residues in contact with VAL 42 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3299 GLU 4.3 1.6 - - - -
3329 GLU 3.2 2.6 - - - +
3339 ILE* 3.0 26.0 + - - -
3369 GLU* 4.5 7.4 - - + +
35h SER* 5.0 14.6 - - - -
40h THR 5.0 0.4 - - - +
41h GLN* 1.3 75.9 - - - +
43h LEU* 1.3 60.2 + - - +
44h ILE* 6.4 0.4 - - + -
54h GLY 2.8 9.5 + - - +
109h VAL* 5.6 3.8 - - + -
110h LEU 3.2 21.1 - - - +
111h ARG* 4.9 3.1 - - + +
114h LEU* 5.6 2.2 - - - -
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Residues in contact with LEU 43 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3289 TYR 3.7 2.0 - - - +
3299 GLU* 2.7 40.2 - - + +
3329 GLU* 1.7 29.8 - - + -
42h VAL* 1.3 68.1 - - - +
44h ILE* 1.3 56.3 + - - -
45h ASN 3.9 2.1 + - - +
108h VAL 4.0 0.2 - - - +
109h VAL* 3.7 0.9 - - - -
110h LEU* 2.8 46.3 + - + +
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Residues in contact with ILE 44 (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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3329 GLU* 1.8 27.0 - - - +
3369 GLU* 4.9 8.7 - - + +
42h VAL* 6.4 0.4 - - + -
43h LEU* 1.3 66.8 - - - +
45h ASN* 1.3 66.2 + - - +
46h CYS* 3.7 4.9 + - + +
51h LYS* 3.1 6.8 - - - -
52h LEU* 2.7 40.0 + - + +
106h VAL* 6.4 2.0 - - + -
108h VAL 3.4 9.4 - - - +
109h VAL* 4.6 5.6 - - + +
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Residues in contact with ASN 45 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43h LEU 3.9 2.8 + - - -
44h ILE* 1.3 75.5 - - - +
46h CYS* 1.3 59.9 + - - +
50h LYS 4.2 2.9 - - - -
51h LYS* 4.6 5.8 - - + +
106h VAL* 4.2 2.9 - - - -
107h ILE* 3.2 20.8 + - + -
108h VAL* 3.0 37.9 + - + +
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Residues in contact with CYS 46 (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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44h ILE* 4.1 6.7 - - + +
45h ASN* 1.3 78.1 - - - +
47h ARG* 1.3 66.5 + - - +
48h ASN* 3.2 6.3 - - + +
49h ASN* 3.1 14.2 + - - -
50h LYS* 3.0 28.3 + - + +
51h LYS* 4.8 0.2 - - - -
52h LEU* 5.2 3.8 - - + +
105h SER* 3.5 11.7 - - - +
106h VAL* 5.7 0.2 - - - -
107h ILE* 4.5 5.5 - - - +
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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