Contacts of the helix formed by residues 93 - 105 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A THR* 1.3 71.9 - - - +
94A ASP* 1.3 60.9 + - - +
96A LYS* 3.7 11.3 - - + +
97A ASN* 2.9 33.0 + - - +
146B PHE* 4.0 19.6 - - + -
161B ARG* 4.9 1.1 + - - -
162B GLU 4.5 3.1 - - - +
163B VAL* 3.1 33.0 - - - +
164B ASP* 3.1 38.9 + - - +
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Residues in contact with ASP 94 (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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6A LEU* 5.6 4.5 - - + -
8A GLU* 3.7 23.8 - - - +
9A VAL 4.0 4.7 - - - +
67A HIS 4.6 6.6 - - - +
68A ARG* 2.8 51.9 + - + +
92A THR* 3.2 1.4 + - - -
93A THR* 1.3 87.7 + - - +
95A ALA* 1.3 59.2 + - - +
97A ASN* 3.8 5.0 - - - +
98A VAL* 2.9 30.1 + - - +
163B VAL* 4.3 10.4 - - - +
168B GLN* 5.4 2.4 - - - +
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Residues in contact with ALA 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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6A LEU* 5.3 4.5 - - + -
8A GLU* 4.5 2.2 + - - +
89A ALA* 4.0 20.0 - - + -
90A PRO 2.9 30.1 - - - +
92A THR* 2.9 10.2 + - - +
94A ASP* 1.3 78.4 - - - +
96A LYS* 1.3 59.3 + - - +
98A VAL* 4.0 6.3 - - - -
99A MET* 2.8 41.7 + - + +
146A THR* 4.4 5.2 - - + -
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Residues in contact with LYS 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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91A ALA* 3.9 26.0 + - - -
92A THR 2.7 23.3 + - - +
93A THR* 3.8 9.0 - - + +
95A ALA* 1.3 71.2 - - - +
97A ASN* 1.3 53.4 + - - +
100A PRO* 3.1 18.9 - - - +
112A SER* 6.1 2.7 - - - +
113A ASP* 3.6 26.9 + - - -
146A THR* 4.9 10.5 - - + +
245A GLY 5.3 6.7 + - - -
247A VAL* 6.0 3.4 - - - +
122B GLN* 5.5 5.1 - - - +
129B ASN* 4.1 26.3 + - + +
133B GLN* 2.7 27.7 + - - -
146B PHE* 4.2 14.4 - - + -
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Residues in contact with ASN 97 (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 ARG 4.5 5.1 - - - +
69A LEU* 5.3 0.3 - - - -
70A ALA* 3.4 24.7 + - - +
93A THR 2.9 17.1 + - - +
94A ASP* 3.8 6.3 - - - +
96A LYS* 1.3 80.5 - - - +
98A VAL* 1.3 59.7 + - - +
100A PRO* 4.1 0.5 - - - +
101A ARG* 4.4 1.4 - - - +
133B GLN* 3.6 12.8 - - - +
143B GLN* 3.2 31.3 + - - +
145B THR* 2.9 29.8 + - - +
146B PHE* 4.5 1.8 - - + -
161B ARG* 3.6 22.9 + - - +
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Residues in contact with VAL 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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6A LEU* 5.0 9.2 - - + -
68A ARG* 5.5 4.9 - - + +
70A ALA* 4.5 14.1 - - - +
73A THR* 4.1 14.1 - - + -
74A ALA* 3.6 34.8 - - + +
77A ILE* 3.9 15.5 - - + -
94A ASP 2.9 27.1 - - - +
95A ALA* 3.9 6.3 - - - +
97A ASN* 1.3 78.8 - - - +
99A MET* 1.3 69.2 + - + +
100A PRO 3.5 0.7 - - - -
101A ARG* 3.2 6.2 + - - +
102A VAL* 3.1 24.4 + - + +
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Residues in contact with MET 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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6A LEU* 5.1 3.6 - - + -
77A ILE* 4.7 18.6 - - - -
87A ILE* 3.5 29.4 - - + +
88A ALA* 3.8 11.7 - - - +
89A ALA* 4.4 9.4 - - + -
95A ALA* 2.8 34.3 + - + +
98A VAL* 1.3 73.2 - - + +
100A PRO* 1.3 66.0 - - + +
102A VAL* 3.1 8.6 + - - +
103A ALA* 2.9 22.7 + - - +
110A VAL* 4.6 6.1 - - + -
144A VAL* 3.5 30.1 - - + +
145A PHE 3.6 12.6 - - - +
146A THR* 4.0 20.9 - - + -
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Residues in contact with PRO 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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96A LYS* 3.1 31.0 - - - +
97A ASN 4.1 1.6 - - - +
98A VAL 3.6 1.3 - - - -
99A MET* 1.3 91.0 - - + +
101A ARG* 1.3 63.2 + - - +
103A ALA* 3.3 8.8 + - + +
104A ALA* 3.0 23.6 + - - +
110A VAL* 4.5 11.2 - - + -
112A SER* 5.5 2.7 - - - +
146A THR* 5.8 1.1 - - + -
129B ASN 3.9 7.4 - - - +
130B ALA* 3.7 34.1 - - + +
133B GLN* 3.7 15.0 - - + +
134B MET* 3.7 8.6 - - + +
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Residues in contact with ARG 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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70A ALA 3.5 24.3 + - - -
71A GLU* 3.8 24.0 + - - +
74A ALA* 3.8 6.8 - - + +
97A ASN 4.4 4.9 - - - +
98A VAL* 3.2 11.3 + - - +
100A PRO* 1.3 78.5 - - - +
102A VAL* 1.3 63.0 + - - +
104A ALA* 3.3 4.9 + - - +
105A LEU* 3.1 40.6 + - + +
172A PRO* 5.6 3.8 - - - +
174A LEU* 4.8 3.4 - - - +
133B GLN* 3.9 8.3 - - + +
136B ALA* 3.7 14.8 + - - +
137B ALA* 3.6 23.1 + - + +
140B GLY* 4.7 6.3 - - - -
141B TRP 3.0 30.1 + - - +
143B GLN* 2.8 42.7 - - - +
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Residues in contact with VAL 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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74A ALA* 3.6 30.3 - - + +
77A ILE* 4.0 26.2 - - + -
78A VAL* 3.9 13.2 - - + +
87A ILE* 5.1 3.6 - - + -
98A VAL* 3.1 22.2 + - + +
99A MET* 3.3 12.1 - - - +
101A ARG* 1.3 75.1 - - - +
103A ALA* 1.3 64.8 + - - +
105A LEU* 2.9 22.6 + - - +
106A LEU* 3.1 25.6 + - + +
144A VAL* 4.5 10.1 - - + -
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Residues in contact with ALA 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 MET 2.9 12.1 + - - +
100A PRO 3.3 8.5 + - - +
102A VAL* 1.3 75.0 - - - +
104A ALA* 1.3 61.6 + - - +
106A LEU 3.1 1.4 + - - -
107A ASP 3.0 4.7 + - - -
108A VAL* 2.8 54.4 + - + +
109A MET 3.6 16.2 - - - +
110A VAL* 4.1 7.9 - - + -
144A VAL* 4.0 14.1 - - + +
134B MET* 4.3 1.8 - - + -
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Residues in contact with ALA 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 PRO 3.0 12.3 + - - +
101A ARG 3.6 8.3 - - - +
102A VAL 3.2 0.2 - - - -
103A ALA* 1.3 76.7 - - - +
105A LEU* 1.3 55.7 + - - +
107A ASP* 2.7 25.4 + - - +
108A VAL 3.9 3.1 + - - -
99B LEU* 4.6 9.3 - - + +
134B MET* 3.8 24.6 - - + +
137B ALA* 3.6 19.5 - - + -
138B ILE* 4.5 13.0 - - + +
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Residues in contact with LEU 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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74A ALA* 4.2 12.1 - - + +
75A ALA* 5.2 1.6 - - - +
78A VAL* 3.8 24.5 - - + +
101A ARG* 3.1 42.5 + - + +
102A VAL* 2.9 12.0 + - - +
104A ALA* 1.3 76.0 - - - +
106A LEU* 1.3 62.1 + - - +
107A ASP* 3.5 1.7 + - - +
137B ALA* 4.3 20.6 - - + +
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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