Contacts of the helix formed by residues 96 - 113 (chain A) in PDB entry 1FFT
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 PRO 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU 4.4 0.7 - - - +
95A PRO* 1.3 86.0 - - + -
97A HIS* 1.3 68.7 + - - +
98A HIS 2.7 3.6 + - - -
99A TYR* 2.8 24.0 + - + -
100A ASP* 2.6 37.0 + - - +
484A SER* 4.6 18.8 - - - +
212B GLY 3.5 2.7 - - - +
213B PRO* 3.3 27.8 - - + -
214B GLY 3.7 10.1 - - - +
216B SER* 5.2 5.2 - - - +
259B GLU* 5.0 1.1 - - - +
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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 LEU* 6.1 1.6 - - + -
95A PRO* 2.5 15.8 + - + +
96A PRO* 1.3 77.0 - - - +
98A HIS* 1.3 88.7 + + + +
100A ASP* 3.2 4.3 + - - -
101A GLN* 3.4 20.6 + - - +
163A GLY 3.6 20.5 + - - -
164A GLU* 4.3 15.5 + - - -
165A PHE 5.9 0.2 - - - -
167A GLN* 3.2 27.1 + - - +
213B PRO* 4.0 9.2 - - + +
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Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.6 32.1 - + + -
94A LEU* 5.6 6.5 - - + +
95A PRO 4.1 2.1 + - - +
96A PRO 2.7 2.6 + - - -
97A HIS* 1.3 105.4 + + + +
99A TYR* 1.3 68.6 + - - +
100A ASP 3.2 1.6 - - - -
101A GLN* 2.9 23.0 + - - +
102A ILE* 2.7 36.6 + - + +
163A GLY* 4.9 8.3 - - - -
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 5.1 11.0 - - + -
82A GLN* 5.2 14.4 - - + -
83A GLN* 3.4 11.8 + - + -
93A PHE* 4.7 7.2 - - + +
94A LEU 5.9 0.4 + - - -
96A PRO* 2.8 20.2 + - + +
98A HIS* 1.3 75.2 - - - +
100A ASP* 1.3 74.2 - - - +
102A ILE* 4.1 7.2 - - - +
103A PHE* 3.2 60.8 + + + +
482A ARG* 3.3 20.9 - - + -
483A LEU 2.9 29.4 + - - -
484A SER* 3.7 25.1 - - - +
1001A HEM 3.4 15.1 + - - -
211B SER* 4.5 0.7 - - - -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 2.6 47.9 + - - +
97A HIS 3.2 0.5 + - - -
99A TYR* 1.3 80.9 - - - +
101A GLN* 1.3 63.9 + - - +
104A THR* 2.4 33.9 + - - +
167A GLN* 2.4 44.6 + - + +
211B SER* 3.3 19.9 + - - +
212B GLY* 3.2 11.7 + - - +
213B PRO* 3.3 2.4 - - - +
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Residues in contact with GLN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A HIS* 3.4 16.3 + - + +
98A HIS* 2.9 36.2 + - - +
100A ASP* 1.3 80.7 - - - +
102A ILE* 1.3 73.0 + - + +
104A THR* 3.4 1.2 - - - -
105A ALA* 2.6 23.3 + - - +
160A LEU* 5.7 1.6 - - + -
163A GLY* 2.7 20.2 + - - +
164A GLU* 3.5 0.3 - - - -
165A PHE* 2.6 61.2 + - + +
166A ALA 3.2 13.3 - - - +
167A GLN* 3.6 1.9 - - + +
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Residues in contact with ILE 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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75A ASP* 4.8 12.1 - - + +
79A MET* 3.1 40.4 - - + -
93A PHE* 3.7 27.6 - - + -
98A HIS* 2.7 32.7 + - + +
99A TYR* 3.8 5.2 - - - +
101A GLN* 1.3 72.3 - - + +
103A PHE* 1.3 54.8 + - - +
104A THR 2.4 15.6 + - - -
105A ALA* 2.5 22.2 + - - +
106A HIS 3.0 8.0 + - - -
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 4.4 7.4 - - + -
79A MET* 2.9 52.2 - - + -
80A ARG* 3.3 17.9 - - - -
83A GLN* 3.9 11.7 - - - -
99A TYR* 3.2 53.5 + + + +
100A ASP* 5.8 0.2 - - - -
102A ILE* 1.3 75.4 - - - +
104A THR* 1.3 60.9 + - - +
106A HIS* 3.4 15.8 - - + +
482A ARG* 5.7 4.5 - - + -
1001A HEM 3.0 76.1 - + + +
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Residues in contact with THR 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 ASP* 2.4 30.5 + - - +
101A GLN 2.9 1.5 + - - -
102A ILE 2.4 14.1 + - - -
103A PHE* 1.3 71.0 - - - +
105A ALA* 1.3 56.2 + - - +
106A HIS 3.1 2.1 + - - -
107A GLY 3.6 2.1 + - - -
108A VAL* 2.7 34.6 + - + +
165A PHE* 5.4 2.0 - - + -
166A ALA 5.5 0.4 - - - -
167A GLN* 4.6 5.8 - - - -
168A THR 4.4 4.9 - - - +
169A GLY* 3.4 33.2 - - - +
170A TRP 3.6 0.2 - - - +
482A ARG* 4.1 11.3 + - - +
1001A HEM 3.0 32.2 + - - +
211B SER* 5.0 2.6 - - - -
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Residues in contact with ALA 105 (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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101A GLN 2.6 15.5 + - - +
102A ILE* 2.5 16.2 + - - +
104A THR* 1.3 67.7 - - - +
106A HIS* 1.3 71.2 + - - +
108A VAL* 3.0 12.9 + - - +
109A ILE* 2.8 30.9 + - + +
156A VAL* 6.6 0.4 - - + -
160A LEU* 4.7 12.1 - - + -
165A PHE* 4.0 23.3 - - + -
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Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY* 4.5 7.2 + - - -
75A ASP* 5.7 4.3 - - + -
76A ALA* 3.3 29.1 - - + +
79A MET* 4.0 13.5 - - + -
102A ILE 3.0 6.0 + - - +
103A PHE* 3.4 16.4 - + - +
105A ALA* 1.3 73.3 - - - +
107A GLY* 1.3 67.0 + - - +
108A VAL 2.5 0.2 + - - -
109A ILE* 2.3 46.4 + - - +
110A MET* 3.3 27.3 + - + +
1001A HEM 2.2 75.1 + + + -
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR 3.6 3.0 + - - -
106A HIS* 1.3 84.5 - - - +
108A VAL* 1.3 59.1 + - - +
109A ILE 3.2 0.2 - - - -
110A MET* 4.2 2.9 - - - -
111A ILE* 2.9 33.3 + - - +
170A TRP* 4.0 6.5 - - - -
1001A HEM 3.3 39.5 - - - +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 2.7 30.0 + - + +
105A ALA* 3.0 14.6 - - - +
106A HIS 2.5 5.7 + - - -
107A GLY* 1.3 74.8 - - - +
109A ILE* 1.3 62.3 + - + +
111A ILE* 4.4 1.0 - - - +
112A PHE* 3.6 21.2 + - + +
113A PHE* 5.2 0.7 - - - -
156A VAL* 6.3 3.4 - - + -
165A PHE* 4.6 10.1 - - + -
169A GLY 4.7 0.4 - - - +
170A TRP* 3.3 34.1 - - - +
190A TRP* 3.8 31.4 - - + +
194A LEU* 5.1 10.0 - - + +
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Residues in contact with ILE 109 (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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68A MET* 3.8 17.5 - - + -
71A ARG* 5.3 6.1 - - + -
72A GLY* 5.1 10.8 - - - -
75A ASP* 4.5 16.8 - - - +
105A ALA* 2.8 25.8 + - + +
106A HIS* 2.3 25.0 + - - +
108A VAL* 1.3 66.1 - - + +
110A MET* 1.3 54.8 + - + +
111A ILE 2.6 18.1 + - - -
112A PHE 2.7 14.4 + - - -
113A PHE* 2.7 21.9 + - + +
114A VAL* 3.3 26.2 - - + -
156A VAL* 4.9 20.9 - - + -
157A ASN* 5.9 1.6 - - - +
160A LEU* 5.8 3.8 - - + -
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Residues in contact with MET 110 (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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69A LEU* 3.5 33.7 - - + -
72A GLY* 4.2 4.7 - - - -
73A PHE* 4.0 27.4 - - + +
106A HIS* 3.3 37.5 + - + +
107A GLY* 4.6 0.2 - - - -
109A ILE* 1.3 80.5 - - + +
111A ILE* 1.3 55.4 + - - +
114A VAL* 4.4 10.1 - - + -
115A ALA* 2.8 36.1 + - - +
1001A HEM 2.9 63.6 - - + +
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Residues in contact with ILE 111 (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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107A GLY 2.9 17.7 - - - +
108A VAL 4.4 0.4 - - - +
109A ILE 2.6 6.1 + - - -
110A MET* 1.3 76.2 - - - +
112A PHE* 1.3 65.2 + - + +
113A PHE 3.7 0.4 - - - -
115A ALA* 4.8 1.0 - - - -
116A MET* 3.3 18.0 + - - +
170A TRP* 3.0 49.1 - - + -
286A GLU* 3.3 32.4 - - + +
290A LEU* 5.1 10.8 - - + +
424A ILE* 6.0 2.0 - - + -
1001A HEM 3.2 41.3 - - + -
1002A HEO 6.0 3.6 - - + -
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Residues in contact with PHE 112 (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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108A VAL* 3.6 12.9 + - + +
109A ILE 2.7 8.1 + - - -
111A ILE* 1.3 86.3 - - + +
113A PHE* 1.3 83.4 + + + +
116A MET* 3.5 23.4 - - - +
149A THR* 4.9 4.2 - - - +
170A TRP* 3.9 17.5 - + - -
171A LEU* 6.1 0.4 - - + -
194A LEU* 3.3 44.9 - - + -
197A SER* 4.3 8.7 + - - +
243A PHE* 5.3 7.2 - + - -
246A LEU* 4.4 8.3 - - + -
282A TRP* 3.5 32.3 - + - -
286A GLU* 2.6 31.2 - - - -
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Residues in contact with PHE 113 (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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64A VAL* 4.5 8.5 - - - +
65A ALA* 4.5 1.0 - - - -
68A MET* 3.5 29.2 - - + +
108A VAL 5.2 1.6 - - - -
109A ILE* 2.7 22.6 + - + +
111A ILE 3.7 0.2 - - - -
112A PHE* 1.3 107.3 - - + +
114A VAL* 1.3 59.3 + - - +
116A MET* 4.0 0.2 - - - +
117A PRO* 3.3 20.0 - - - +
149A THR* 3.6 9.8 - - + +
152A GLY* 3.0 24.7 - - - -
153A VAL* 3.0 49.6 - - + -
156A VAL* 4.0 13.5 - - + -
193A SER 4.2 2.0 - - - -
194A LEU* 4.2 12.8 - - + -
197A SER* 3.8 22.7 - - - -
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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