Contacts of the helix formed by residues 116 - 132 (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 MET 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE 3.3 25.0 + - - +
112A PHE* 3.5 24.0 - - - +
114A VAL 4.0 0.2 - - - +
115A ALA* 1.3 79.9 - - - +
117A PRO* 1.4 70.0 - - + +
118A PHE 3.0 1.7 + - - -
119A VAL* 3.3 31.6 - - + +
120A ILE* 3.6 25.9 - - + +
149A THR* 5.5 4.5 - - + -
197A SER* 6.0 0.9 - - - +
201A THR* 4.2 16.4 - - + +
243A PHE* 5.0 11.9 - - + -
286A GLU* 4.5 18.6 - - - +
289A ILE* 4.8 9.2 - - + -
290A LEU* 4.2 7.4 - - + -
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Residues in contact with PRO 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.0 29.2 - - + -
62A ILE* 5.1 1.6 - - - +
64A VAL* 5.2 5.4 - - + -
65A ALA* 4.2 21.1 - - + +
113A PHE* 3.3 23.8 - - - +
114A VAL* 3.5 12.1 - - - -
115A ALA 3.5 2.9 - - - -
116A MET* 1.4 97.6 - - + +
118A PHE* 1.3 51.1 + - - +
120A ILE* 4.5 3.6 - - + -
121A GLY* 2.3 41.7 + - - -
149A THR* 5.2 10.5 - - + -
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 6.3 2.0 - - - -
65A ALA* 5.7 0.6 - - - +
114A VAL 4.9 1.4 + - - +
115A ALA* 3.2 21.6 + - - +
116A MET 3.0 0.8 + - - -
117A PRO* 1.3 75.3 - - - +
119A VAL* 1.3 78.0 + - + +
121A GLY* 4.9 0.2 - - - -
122A LEU* 2.6 63.4 + - + +
290A LEU* 4.5 12.1 - - + -
293A PRO* 4.4 7.2 - - + -
294A VAL* 3.3 49.6 - - + -
297A VAL* 4.9 1.8 - - + -
428A VAL* 4.6 8.5 - - + -
431A GLY* 3.7 2.0 - - - -
432A CYS* 3.0 56.8 - - + -
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A MET* 3.3 33.9 - - + +
118A PHE* 1.3 88.4 - - + +
120A ILE* 1.3 73.0 + - + +
121A GLY 3.0 5.4 + - - -
122A LEU* 4.9 1.1 - - - -
123A MET* 3.1 54.6 + - + +
235A ALA* 5.2 0.4 - - + -
239A ILE* 5.5 2.0 - - + -
289A ILE* 3.9 23.8 - - + +
290A LEU* 4.7 4.5 - - + -
293A PRO* 3.4 26.7 - - + -
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Residues in contact with ILE 120 (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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61A TYR* 3.2 39.0 - - + +
116A MET* 3.6 32.3 - - + +
117A PRO* 3.1 4.2 + - + +
119A VAL* 1.3 83.9 - - + +
121A GLY* 1.3 58.4 + - - +
123A MET* 4.8 0.7 - - + -
124A ASN* 3.1 19.2 - - - +
145A SER 5.2 1.1 - - - +
149A THR* 4.8 5.6 - - + +
201A THR* 2.7 43.7 - - + +
204A THR* 3.5 36.0 - - + +
239A ILE* 5.4 2.0 - - + -
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Residues in contact with GLY 121 (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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58A GLY* 3.8 5.3 - - - -
61A TYR* 3.6 23.1 - - - -
62A ILE* 4.4 9.9 - - - -
117A PRO 2.3 24.8 + - - -
118A PHE 3.6 0.2 - - - -
120A ILE* 1.3 72.7 - - - +
122A LEU* 1.3 59.0 + - - +
124A ASN* 2.7 26.2 + - - +
125A LEU* 3.1 5.4 + - - +
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Residues in contact with LEU 122 (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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62A ILE* 4.7 14.9 - - + +
118A PHE* 2.6 43.6 + - + +
119A VAL* 4.6 2.0 - - - +
121A GLY* 1.3 66.4 - - - +
123A MET* 1.3 55.2 + - - +
124A ASN 2.8 4.3 - - - -
125A LEU* 2.7 29.5 + - + +
126A VAL* 3.0 17.7 + - + +
228A PHE* 3.9 11.0 - - + -
297A VAL* 3.3 36.1 - - + -
432A CYS* 5.5 3.8 - - - +
435A GLY* 5.2 4.5 - - - -
436A MET* 5.6 7.0 - - - +
439A TRP* 4.1 22.2 - - + -
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Residues in contact with MET 123 (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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119A VAL* 3.1 44.9 + - + +
120A ILE* 4.6 3.4 - - + +
122A LEU* 1.3 78.5 - - - +
124A ASN* 1.3 60.7 + - - +
125A LEU 3.4 0.3 + - - -
127A VAL* 3.3 33.4 + - + +
128A PRO* 3.6 1.7 - - - +
204A THR* 4.8 9.6 - - + -
208A PHE* 3.1 21.5 - - + -
228A PHE* 3.7 11.6 - - + -
232A SER* 3.2 36.8 - - - +
236A ASN* 3.2 37.5 - - - +
239A ILE* 5.2 4.3 - - + -
293A PRO* 4.4 5.6 - - + -
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Residues in contact with ASN 124 (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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54A HIS* 3.0 31.1 + - - +
57A LEU* 2.9 14.1 + - - +
58A GLY* 2.5 36.0 - - - +
61A TYR* 4.1 8.8 + - - -
120A ILE 3.1 19.8 + - - +
121A GLY* 2.7 14.7 + - - +
122A LEU 2.8 1.2 + - - -
123A MET* 1.3 81.6 - - - +
125A LEU* 1.3 55.7 + - - -
128A PRO* 4.4 1.6 - - - +
142A ASN* 3.2 23.7 + - - +
208A PHE* 3.3 21.3 - - + -
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Residues in contact with LEU 125 (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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54A HIS* 5.4 0.4 - - - -
55A LYS* 3.5 19.5 - - + +
58A GLY* 3.7 13.5 - - - -
59A ILE* 3.4 44.2 - - + +
62A ILE* 5.7 3.4 - - + -
121A GLY 3.1 3.2 + - - +
122A LEU* 2.7 18.8 + - + +
124A ASN* 1.3 74.4 - - - +
126A VAL* 1.3 73.5 + - + +
127A VAL 4.0 0.4 - - - -
128A PRO* 4.3 3.8 - - - +
129A LEU* 4.5 18.9 - - + +
439A TRP* 5.2 6.7 - - + -
442A LYS* 5.2 6.5 - - + +
443A ALA* 3.7 23.6 - - + -
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Residues in contact with VAL 126 (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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122A LEU* 3.0 12.9 + - + +
125A LEU* 1.3 102.6 - - + +
127A VAL* 1.3 66.6 + - - +
128A PRO* 3.3 3.1 - - - -
129A LEU* 4.0 4.6 + - - +
130A GLN* 3.7 20.6 + - - +
228A PHE* 4.3 6.1 - - + -
439A TRP* 3.1 52.9 - - + +
442A LYS* 6.2 0.4 - - + -
540A GLU* 3.1 30.7 - - - +
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Residues in contact with VAL 127 (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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123A MET* 3.3 40.4 + - + +
126A VAL* 1.3 74.9 - - - +
128A PRO* 1.3 71.7 - - + +
130A GLN* 3.7 5.0 + - - +
131A ILE* 3.1 23.8 + - + +
208A PHE* 4.8 8.7 - - + -
211A THR* 5.9 2.9 - - + -
212A ILE* 4.2 21.1 - - + -
228A PHE* 3.6 17.9 - - + +
229A THR* 3.6 22.7 - - + -
232A SER* 3.6 12.3 - - - +
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Residues in contact with PRO 128 (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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54A HIS* 3.2 39.7 - - + +
123A MET 3.6 9.6 - - - +
124A ASN 4.4 2.7 - - - +
125A LEU 4.3 0.9 - - - -
126A VAL* 3.4 9.2 - - - +
127A VAL* 1.3 90.3 - - + +
129A LEU* 1.3 55.9 + - + +
130A GLN 2.5 18.5 + - - -
131A ILE* 2.8 30.5 + - + +
132A GLY 3.2 4.2 + - - -
133A ALA* 4.0 10.6 + - + -
135A ASP* 3.6 17.3 - - - +
136A VAL* 5.4 1.3 - - + -
208A PHE* 5.1 6.3 - - + -
211A THR* 5.7 5.6 - - + -
551A ASN* 6.0 0.2 - - - +
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Residues in contact with LEU 129 (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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54A HIS* 4.2 3.8 - - - +
55A LYS* 3.7 15.3 - - + -
125A LEU* 4.5 14.6 - - + +
126A VAL* 4.0 5.1 + - - +
127A VAL 3.8 0.2 - - - -
128A PRO* 1.3 76.7 - - + +
130A GLN* 1.3 57.7 + - - +
132A GLY* 4.3 2.7 - - - -
133A ALA 5.3 2.7 - - - +
442A LYS* 4.8 19.7 - - + +
539A LEU* 3.5 8.8 - - - +
540A GLU* 2.9 34.4 + - + +
543A THR* 5.4 4.0 - - + +
547A PRO* 3.8 25.6 - - + -
551A ASN* 3.1 41.5 - - - +
552A PHE* 4.2 19.6 - - + +
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Residues in contact with GLN 130 (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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126A VAL* 3.7 20.0 + - - +
127A VAL* 3.7 6.9 + - - +
128A PRO 2.5 7.9 + - - -
129A LEU* 1.3 75.6 - - - +
131A ILE* 1.3 64.5 + - + +
132A GLY 3.2 1.6 - - - -
220A MET* 4.8 4.0 - - - +
226A PRO* 3.0 27.5 - - + +
228A PHE* 4.1 14.6 - - - +
229A THR* 3.0 22.7 + - - +
300A GLU* 4.4 9.7 + - - -
538A THR* 3.7 19.8 + - - +
539A LEU* 3.5 16.6 + - - +
540A GLU* 3.0 38.8 + - + +
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Residues in contact with ILE 131 (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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127A VAL* 3.1 19.5 - - + +
128A PRO* 2.8 18.3 + - + +
130A GLN* 1.3 81.7 - - + +
132A GLY* 1.3 57.0 - - - +
133A ALA* 4.2 7.0 - - + -
211A THR* 4.3 20.2 - - + +
212A ILE* 5.0 3.1 - - + -
215A MET 3.2 28.5 - - - +
216A ARG* 3.6 24.4 - - + +
217A ALA* 2.6 39.4 + - - +
220A MET* 4.4 9.5 - - - +
225A MET* 6.2 0.2 - - + -
226A PRO* 4.9 4.3 - - + -
229A THR* 3.5 30.1 - - + +
539A LEU* 4.3 0.9 - - - -
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Residues in contact with GLY 132 (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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128A PRO 3.2 2.8 + - - -
129A LEU 4.9 1.3 - - - -
130A GLN 3.2 3.2 - - - +
131A ILE* 1.3 80.1 - - - +
133A ALA* 1.3 61.1 + - - +
216A ARG 3.2 21.6 - - - +
217A ALA* 3.9 5.4 - - - -
218A PRO* 4.6 3.1 - - - +
539A LEU* 3.3 24.5 - - - -
552A PHE* 4.6 8.5 - - - -
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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