Contacts of the helix formed by residues 93 - 105 (chain C) in PDB entry 1EFP
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 THR 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C THR* 1.3 72.0 - - - +
94C ASP* 1.3 64.2 + - - +
96C LYS* 3.1 10.4 + - + +
97C ASN* 2.8 34.1 + - - +
146D PHE* 4.0 20.7 - - + -
161D ARG* 5.5 0.9 - - - -
162D GLU 4.5 3.8 - - - +
163D VAL* 3.3 32.0 - - - +
164D ASP* 3.0 39.0 + - - +
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Residues in contact with ASP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 5.7 4.5 - - + -
8C GLU* 4.0 22.9 - - - +
9C VAL 4.0 5.0 - - - +
67C HIS 4.4 8.9 - - - +
68C ARG* 3.0 48.2 + - + +
92C THR* 3.2 1.0 + - - -
93C THR* 1.3 86.2 + - - +
95C ALA* 1.3 59.9 + - - +
97C ASN* 3.6 5.6 + - - +
98C VAL* 2.8 31.1 + - + +
161D ARG* 5.8 2.5 + - - +
163D VAL* 4.5 10.4 - - - +
168D GLN* 5.3 2.9 - - - +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 5.3 4.7 - - + -
8C GLU* 5.1 2.0 - - - +
89C ALA* 3.9 20.4 - - + -
90C PRO* 2.9 31.0 - - + +
91C ALA* 4.7 1.3 - - - -
92C THR* 3.0 8.4 + - - +
94C ASP* 1.3 77.5 - - - +
96C LYS* 1.3 59.5 + - - +
97C ASN 3.1 1.8 - - - -
98C VAL* 4.2 5.4 - - - -
99C MET* 2.8 41.9 + - + +
146C THR* 5.2 3.4 - - - -
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Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ALA* 4.1 25.9 + - + -
92C THR 2.7 27.1 + - - +
93C THR* 3.7 7.6 - - + +
95C ALA* 1.3 73.0 - - - +
97C ASN* 1.3 57.3 + - - +
99C MET* 5.1 0.2 - - - -
100C PRO* 3.0 16.6 - - - +
112C SER* 6.2 3.1 - - - -
113C ASP* 3.9 25.1 + - - -
146C THR* 5.1 10.8 - - + -
243C GLN 5.8 1.6 + - - -
245C GLY 5.3 6.9 + - - -
247C VAL* 6.0 4.2 - - - +
122D GLN* 5.5 5.7 - - - +
129D ASN* 4.1 26.6 + - + +
133D GLN* 2.9 23.3 + - - -
146D PHE* 4.3 12.8 - - + -
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Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG 4.5 5.5 - - - +
69C LEU* 5.3 0.2 - - - -
70C ALA* 3.6 24.1 + - - +
93C THR 2.8 16.9 + - - +
94C ASP* 3.8 7.4 - - - +
96C LYS* 1.3 78.9 - - - +
98C VAL* 1.3 60.4 + - - +
100C PRO* 4.1 0.7 - - - +
101C ARG* 4.4 1.6 - - - +
133D GLN* 3.6 12.5 - - - +
143D GLN* 2.9 38.7 + - - +
145D THR* 2.9 27.8 + - - +
146D PHE* 4.3 4.6 - - + -
161D ARG* 3.4 23.7 + - - +
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 5.3 7.9 - - + -
68C ARG* 5.5 6.3 - - + +
70C ALA* 4.4 14.8 - - - -
73C THR* 4.1 18.2 - - + -
74C ALA* 3.6 35.0 - - + +
77C ILE* 4.1 9.2 - - + -
94C ASP* 2.8 28.9 - - + +
95C ALA* 4.1 4.5 - - - +
97C ASN* 1.3 76.1 - - + +
99C MET* 1.3 68.5 + - + +
100C PRO 3.5 0.9 - - - -
101C ARG* 3.2 7.1 + - - +
102C VAL* 3.1 24.8 + - + +
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Residues in contact with MET 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 5.0 2.7 - - - -
77C ILE* 4.7 19.3 - - - -
87C ILE* 3.8 21.5 - - + +
88C ALA* 3.8 10.5 - - - +
89C ALA* 4.3 12.3 - - + -
95C ALA* 2.8 41.6 + - + +
98C VAL* 1.3 74.6 - - - +
100C PRO* 1.3 66.7 - - + +
102C VAL* 3.0 9.5 + - + +
103C ALA* 3.0 21.5 + - - +
110C VAL* 4.6 4.7 - - + -
144C VAL* 3.4 34.9 - - + +
145C PHE 3.5 22.7 - - - +
146C THR* 4.4 14.1 - - + -
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Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LYS* 3.0 31.0 - - - +
97C ASN 4.1 2.0 - - - +
98C VAL 3.6 1.3 - - - -
99C MET* 1.3 90.7 - - + +
101C ARG* 1.3 62.8 + - - +
103C ALA* 3.4 4.2 + - + +
104C ALA* 3.1 23.2 + - - +
110C VAL* 4.3 15.7 - - + -
112C SER* 5.4 2.7 - - - +
129D ASN 3.8 9.9 - - - +
130D ALA* 3.7 33.4 - - + +
133D GLN* 3.6 13.5 - - + +
134D MET* 3.7 9.1 - - + +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ALA* 3.8 10.1 - - - -
71C GLU* 3.4 28.3 + - - +
74C ALA* 3.7 21.0 - - + +
97C ASN 4.4 4.3 - - - +
98C VAL 3.2 10.9 + - - +
99C MET 3.2 0.2 - - - -
100C PRO* 1.3 79.1 - - - +
102C VAL* 1.3 64.0 + - - +
104C ALA* 3.2 5.4 + - - +
105C LEU* 3.0 31.1 + - + +
174C LEU* 4.3 6.7 - - - +
133D GLN* 4.0 7.0 - - + +
136D ALA* 3.4 17.4 + - - +
137D ALA* 3.6 23.8 + - + +
140D GLY* 4.6 4.8 - - - -
141D TRP 3.0 31.1 + - - +
143D GLN* 2.7 42.9 - - - +
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Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 3.7 30.5 - - - +
77C ILE* 4.2 26.7 - - + -
78C VAL* 3.8 13.0 - - + +
87C ILE* 4.9 3.8 - - + -
98C VAL* 3.1 21.2 + - + +
99C MET* 3.0 11.6 + - + +
101C ARG* 1.3 76.5 - - - +
103C ALA* 1.3 65.2 + - - +
105C LEU* 3.0 20.6 + - - +
106C LEU* 3.1 26.4 + - + +
144C VAL* 4.5 10.8 - - + -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MET 3.0 11.8 + - - +
100C PRO 3.7 7.9 - - - +
101C ARG 3.3 0.2 - - - -
102C VAL* 1.3 74.8 - - - +
104C ALA* 1.3 58.2 + - - +
106C LEU* 3.2 1.1 + - - -
107C ASP 2.9 8.1 + - - -
108C VAL* 2.8 55.2 + - + +
109C MET 3.4 17.3 - - - +
110C VAL* 4.1 5.2 - - + -
144C VAL* 4.0 14.1 - - + -
134D MET* 4.1 4.5 - - + -
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PRO 3.1 13.4 + - - +
101C ARG 3.5 8.7 - - - +
103C ALA* 1.3 77.3 - - - +
105C LEU* 1.3 58.6 - - - +
107C ASP* 2.8 20.0 + - - +
108C VAL 4.4 2.9 - - - -
99D LEU* 4.5 9.0 - - + +
134D MET* 3.7 25.1 - - + +
137D ALA* 3.6 19.7 - - + -
138D ILE* 4.2 15.2 - - + +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ALA* 4.0 11.9 - - + +
75C ALA* 5.1 2.0 - - - +
78C VAL* 3.7 32.7 - - + +
101C ARG* 3.0 38.2 + - + +
102C VAL* 3.0 10.9 + - - +
104C ALA* 1.3 76.9 - - - +
106C LEU* 1.3 60.0 + - - +
107C ASP* 3.3 4.5 + - - +
137D ALA* 4.5 18.8 - - + +
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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