Contacts of the helix formed by residues 94 - 104 (chain A) 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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 5.0 1.5 + - - +
91A ALA* 3.9 9.7 + - - +
92A LEU 3.4 0.6 - - - -
93A LYS* 1.3 78.5 - - + +
95A MET* 1.3 61.4 + - - +
96A PRO 3.6 2.2 - - - -
97A HIS* 3.4 26.8 + - + +
98A ALA* 3.4 7.8 + - - +
649A GLU* 5.7 0.7 - - - -
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.7 11.5 + - - +
92A LEU* 3.6 16.1 + - - +
93A LYS 3.4 3.0 - - - -
94A TYR* 1.3 74.5 - - - +
96A PRO* 1.4 59.6 - - - +
98A ALA* 2.9 11.0 + - - +
99A VAL* 2.9 26.2 + - - +
500A GLY* 6.6 0.2 - - - -
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Residues in contact with PRO 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS 4.8 3.3 - - - +
94A TYR 3.6 0.2 - - - -
95A MET* 1.4 75.7 - - - +
97A HIS* 1.3 57.7 + - - +
99A VAL* 4.1 9.9 - - + +
100A LEU* 2.9 33.3 + - - +
641A MET* 5.5 3.7 - - + +
645A THR* 3.9 31.7 - - - +
648A LEU* 6.1 3.8 - - + -
649A GLU* 5.7 3.4 - - + +
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.4 22.3 + - + +
95A MET 3.2 0.8 - - - -
96A PRO* 1.3 77.5 - - - +
98A ALA* 1.3 57.0 + - - +
100A LEU* 4.4 3.8 - - - +
101A LYS* 3.8 17.8 + - - +
128A PHE* 5.5 3.1 - - - +
645A THR* 4.6 6.1 - - - -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR 3.4 7.2 + - - +
95A MET* 2.9 12.8 + - - +
97A HIS* 1.3 78.7 - - - +
99A VAL* 1.3 58.9 + - - +
100A LEU 3.3 0.4 - - - -
101A LYS* 3.5 3.9 + - - +
102A LEU* 2.9 28.8 + - - +
126A ILE* 5.5 7.0 - - + -
127A SER 4.4 20.9 - - - +
128A PHE* 4.5 13.7 - - + +
129A VAL* 5.3 2.8 + - - +
496A VAL* 5.4 9.6 - - + -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET 2.9 15.0 + - - +
96A PRO* 3.4 9.2 + - + -
98A ALA* 1.3 73.9 - - - +
100A LEU* 1.3 59.7 + - - +
102A LEU* 3.3 7.5 + - - +
103A LEU* 2.9 30.8 + - - +
550A VAL* 5.8 7.6 - - + +
551A LEU* 6.5 0.7 - - - -
554A THR* 5.4 13.4 - - - -
641A MET* 5.8 0.7 - - - -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565 C 6.2 4.9 - - - -
96A PRO 2.9 19.9 + - - +
97A HIS* 4.7 4.0 - - - +
99A VAL* 1.3 77.2 - - - +
101A LYS* 1.3 57.5 + - - +
103A LEU* 3.3 5.0 + - - +
104A GLU* 2.9 29.0 + - - +
638A LEU* 6.0 1.1 - - - +
641A MET* 4.4 30.6 - - + +
642A ARG* 5.2 3.4 - - - +
645A THR* 5.0 3.4 - - - -
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575 G 6.1 0.9 - - - +
97A HIS 3.8 17.0 + - - +
98A ALA* 3.5 4.8 + - - +
99A VAL 3.4 0.4 - - - -
100A LEU* 1.3 76.0 - - - +
102A LEU* 1.3 64.7 + - - +
104A GLU* 3.8 12.0 + - - +
105A ASN* 3.8 13.5 + - - +
128A PHE* 6.3 0.7 - - + -
129A VAL* 3.4 33.1 - - - +
131A GLU 5.0 6.4 - - - +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA 2.9 19.1 + - - +
99A VAL* 3.4 10.8 - - - +
100A LEU 3.2 0.2 - - - -
101A LYS* 1.3 76.4 - - - +
103A LEU* 1.3 58.6 + - - +
105A ASN* 3.0 26.7 + - - +
106A MET* 3.9 1.7 + - - -
129A VAL* 5.0 8.3 - - + +
493A GLY* 6.3 2.9 - - - -
554A THR* 6.2 3.1 - - - -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 2.9 19.0 + - - +
100A LEU* 4.1 4.0 - - - +
102A LEU* 1.3 72.8 - - - +
104A GLU* 1.3 60.0 + - - +
105A ASN 3.3 0.6 + - - -
106A MET* 4.0 15.7 + - - +
554A THR* 6.3 2.7 - - - -
637A TRP 6.0 1.6 - - - +
638A LEU* 5.3 13.6 - - + +
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU 2.9 17.4 + - - +
101A LYS* 4.0 10.8 - - - +
102A LEU 3.1 0.6 + - - -
103A LEU* 1.3 79.1 - - - +
105A ASN* 1.3 57.4 + - + +
106A MET 3.6 1.5 + - - -
131A GLU 5.5 5.4 - - - +
133A PRO* 4.2 20.8 - - + +
421A ALA* 4.6 8.3 - - - +
422A LEU* 5.8 3.5 + - + -
638A LEU* 5.6 7.6 - - + +
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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