Contacts of the helix formed by residues 96 - 115 (chain Y) 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 LYS 96 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Y ASN* 3.6 7.1 - - + +
95Y GLY* 1.3 75.8 - - - +
97Y ASN* 1.3 63.4 + - - +
98Y ALA 3.3 2.0 - - - -
99Y ARG* 3.2 21.2 + - - +
100Y GLU* 3.6 6.6 + - - +
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Residues in contact with ASN 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Y ILE* 5.0 16.6 - - + -
93Y LEU* 4.3 17.9 - - + -
94Y ASN* 5.2 4.2 - - + +
95Y GLY 3.6 1.8 - - - +
96Y LYS* 1.3 78.1 - - - +
98Y ALA* 1.3 57.6 + - - +
100Y GLU* 3.6 4.9 + - - +
101Y PHE* 2.9 29.4 + - - +
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Residues in contact with ALA 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y GLN* 4.4 9.6 - - + +
89Y LEU* 3.7 43.1 - - + +
90Y THR* 3.9 9.6 - - - +
93Y LEU* 4.7 3.7 - - + +
95Y GLY 4.3 8.1 + - - +
96Y LYS 3.3 0.4 - - - -
97Y ASN* 1.3 75.4 - - - +
99Y ARG* 1.3 60.8 + - - +
101Y PHE* 3.7 7.7 - - - +
102Y MET* 2.9 31.0 + - - +
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Residues in contact with ARG 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Y GLY 4.2 7.6 + - - +
96Y LYS* 3.2 16.4 + - - +
98Y ALA* 1.3 80.3 - - - +
100Y GLU* 1.3 57.4 + - - +
102Y MET* 3.8 3.9 - - - +
103Y GLY* 2.9 23.2 + - - -
1x MET* 6.0 7.2 - - + -
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Residues in contact with GLU 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Y LYS 3.6 6.2 + - - +
97Y ASN* 3.6 6.0 + - - +
99Y ARG* 1.3 76.1 - - - +
101Y PHE* 1.3 59.4 + - - +
103Y GLY* 3.6 3.7 - - - +
104Y GLU* 2.9 30.8 + - - +
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Residues in contact with PHE 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Y LEU* 6.1 1.8 - - + -
97Y ASN 2.9 21.0 + - - +
98Y ALA* 3.7 9.2 - - - +
99Y ARG 3.2 0.2 - - - -
100Y GLU* 1.3 77.0 - - - +
102Y MET* 1.3 57.1 + - - +
104Y GLU* 3.4 3.6 + - - +
105Y LEU* 2.9 31.6 + - - +
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Residues in contact with MET 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Y LEU* 6.1 4.5 - - + -
82Y SER 6.0 1.1 - - - +
86Y GLN* 5.4 13.0 - - + -
98Y ALA 2.9 18.0 + - - +
99Y ARG* 3.9 3.6 - - - +
101Y PHE* 1.3 76.2 - - - +
103Y GLY* 1.3 57.1 + - - +
105Y LEU* 4.4 4.5 - - - +
106Y TRP* 2.9 36.8 + - + +
1x MET* 6.4 2.9 - - + -
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Residues in contact with GLY 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Y ARG 2.9 16.1 + - - -
100Y GLU* 3.4 4.9 + - - -
101Y PHE 3.3 0.4 - - - -
102Y MET* 1.3 76.6 - - - +
104Y GLU* 1.3 57.7 + - - +
106Y TRP* 4.5 3.8 - - - +
107Y PRO* 4.7 10.7 - - - +
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Residues in contact with GLU 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Y GLU 2.9 16.5 + - - +
101Y PHE* 4.1 3.8 - - - +
103Y GLY* 1.3 79.6 - - - +
105Y LEU* 1.3 62.2 + - - +
106Y TRP 3.3 2.4 + - - -
107Y PRO* 4.2 1.9 - - - +
108Y LEU* 4.0 19.4 + - - +
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Residues in contact with LEU 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Y PHE 2.9 18.5 + - - +
102Y MET* 4.2 4.0 - - - +
104Y GLU* 1.3 77.3 - - - +
106Y TRP* 1.3 63.8 + - - +
108Y LEU* 4.4 3.6 - - - +
109Y LEU* 3.6 19.4 + - - +
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Residues in contact with TRP 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y CYS 5.2 9.6 - - - +
34Y LEU* 5.6 8.5 - - + -
102Y MET* 2.9 20.3 + - + +
103Y GLY* 5.0 3.1 - - - -
104Y GLU 3.3 0.2 - - - -
105Y LEU* 1.3 77.3 - - - +
107Y PRO* 1.4 60.8 - - - +
109Y LEU* 3.1 8.7 + - - +
110Y LEU* 3.0 24.8 + - - +
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Residues in contact with PRO 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Y GLY 4.7 9.5 - - - +
104Y GLU 4.2 3.7 - - - +
106Y TRP* 1.4 76.9 - - - +
108Y LEU* 1.3 58.0 + - - +
110Y LEU* 3.8 9.2 - - + +
111Y SER* 2.8 30.0 + - - -
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Residues in contact with LEU 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Y GLU 4.0 16.9 + - - +
105Y LEU* 4.4 4.3 - - - +
106Y TRP 3.2 0.8 - - - -
107Y PRO* 1.3 75.4 - - - +
109Y LEU* 1.3 59.8 + - - +
111Y SER* 4.4 2.0 - - - +
112Y ALA* 2.9 30.8 + - - +
120Y PRO* 3.3 24.3 - - + +
122Y ALA* 6.0 4.3 - - + -
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Residues in contact with LEU 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Y VAL* 6.1 5.8 - - + -
43Y VAL* 5.3 1.6 - - - +
105Y LEU 3.6 12.0 + - - +
106Y TRP* 3.1 10.6 + - - +
108Y LEU* 1.3 79.0 - - - +
110Y LEU* 1.3 56.8 + - - +
112Y ALA* 3.4 5.4 + - - +
113Y GLN* 2.9 30.8 + - - +
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Residues in contact with LEU 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y LYS* 6.5 1.1 - - + -
106Y TRP 3.0 13.7 + - - +
107Y PRO* 3.8 11.4 - - + +
109Y LEU* 1.3 77.7 - - - +
111Y SER* 1.3 56.2 + - - +
113Y GLN* 3.3 4.1 + - - +
114Y GLU* 2.9 31.0 + - - +
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Residues in contact with SER 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Y PRO 2.8 21.5 + - - -
108Y LEU* 4.0 4.5 - - - -
110Y LEU* 1.3 73.1 - - - +
112Y ALA* 1.3 59.4 + - - +
114Y GLU* 4.1 6.9 - - - +
115Y ASN* 3.7 17.7 + - - +
119Y ILE 4.1 3.5 - - - +
120Y PRO* 4.3 2.6 - - - +
121Y SER* 4.3 24.4 + - - -
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Residues in contact with ALA 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Y LYS 3.8 0.4 - - - +
43Y VAL* 4.7 7.6 - - + -
108Y LEU 2.9 18.6 + - - +
109Y LEU* 3.9 5.6 - - - +
111Y SER* 1.3 76.6 - - - +
113Y GLN* 1.3 58.6 + - - +
114Y GLU 3.3 0.4 - - - -
115Y ASN* 3.1 20.3 + - - +
118Y GLY* 3.3 27.4 + - - +
119Y ILE 3.6 11.7 - - - -
120Y PRO* 3.5 19.7 - - + +
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Residues in contact with GLN 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y VAL* 6.0 4.7 - - + -
39Y ASP* 4.6 13.5 - - + +
42Y LYS* 4.0 31.5 - - + +
43Y VAL* 4.9 4.0 - - + +
109Y LEU 2.9 18.1 + - - +
110Y LEU* 3.3 4.2 + - - +
112Y ALA* 1.3 73.3 - - - +
114Y GLU* 1.3 63.3 + - - +
115Y ASN 3.2 6.3 - - - +
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Residues in contact with GLU 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y LEU 2.9 16.8 + - - +
111Y SER* 4.4 6.3 - - - +
112Y ALA 3.3 0.2 - - - -
113Y GLN* 1.3 77.6 - - - +
115Y ASN* 1.3 60.7 + - - +
116Y ILE 4.0 0.9 + - - -
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Residues in contact with ASN 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42Y LYS* 4.1 5.7 - - - +
111Y SER 3.7 12.1 + - - +
112Y ALA 3.1 22.3 + - - +
113Y GLN 3.2 7.7 - - - +
114Y GLU* 1.3 82.3 - - - +
116Y ILE* 1.3 63.6 + - - +
117Y ALA* 4.1 9.2 - - + +
118Y GLY 4.0 4.7 + - - +
119Y ILE 4.5 9.2 - - - +
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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