Contacts of the helix formed by residues 86 - 103 (chain A) in PDB entry 4MEI
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 ASP 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A TYR* 1.3 75.1 - - - +
87A GLU* 1.3 75.7 + - - +
88A ALA* 3.2 19.4 + - - +
89A ILE* 3.3 15.7 + - + +
90A THR* 3.1 23.3 + - - -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR 3.6 3.4 + - - -
86A ASP* 1.3 76.8 + - - +
88A ALA* 1.3 61.5 + - - +
90A THR* 3.1 7.2 + - - -
91A ARG* 2.7 54.7 + - - +
158A PHE* 3.8 29.2 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.1 15.2 + - - +
87A GLU* 1.3 80.3 - - - +
89A ILE* 1.3 58.8 + - - +
91A ARG* 3.4 10.5 + - - +
92A TYR* 3.0 27.2 + - - +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.2 14.1 - - + -
86A ASP* 3.3 21.0 + - + +
88A ALA* 1.3 80.2 - - - +
90A THR* 1.3 65.4 + - - +
92A TYR* 3.4 16.2 - - + +
93A PHE* 3.2 51.1 + - + -
192A TYR* 3.8 12.8 - - + +
207A LEU* 4.3 17.0 - - + -
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Residues in contact with THR 90 (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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85A TYR* 4.6 2.8 + - - +
86A ASP 3.1 12.1 + - - -
87A GLU* 3.1 12.1 + - - -
89A ILE* 1.3 77.8 - - - +
91A ARG* 1.3 64.3 + - - +
93A PHE* 3.4 1.6 + - - -
94A ALA* 3.1 21.1 + - - +
158A PHE* 4.2 9.2 - - + -
164A ILE* 3.8 17.0 - - + -
190A PHE* 3.6 32.5 - - + -
192A TYR* 2.4 31.0 + - - +
209A PHE* 4.3 5.6 - - + -
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Residues in contact with ARG 91 (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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87A GLU* 2.7 53.4 + - - +
88A ALA* 3.6 10.8 - - - +
90A THR* 1.3 73.4 - - - +
92A TYR* 1.3 67.3 + - - +
94A ALA* 3.2 1.5 + - - +
95A SER* 2.9 22.1 + - - -
156A ILE* 2.7 64.3 + - + +
157A SER* 4.4 6.1 - - - +
158A PHE* 3.6 17.3 - - + -
164A ILE* 5.7 0.2 - - - -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 3.0 14.6 + - - +
89A ILE* 3.4 18.2 - - + +
91A ARG* 1.3 80.8 - - - +
93A PHE* 1.3 89.4 + + - +
95A SER* 3.4 6.4 + - - -
96A GLN* 3.1 56.9 + - + +
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Residues in contact with PHE 93 (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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89A ILE* 3.2 44.8 + - + +
91A ARG 3.3 0.4 - - - -
92A TYR* 1.3 99.8 - + - +
94A ALA* 1.3 61.4 + - - +
96A GLN* 3.3 12.8 + - - +
97A TYR* 2.8 29.6 + - - +
119A LEU* 4.0 18.0 - - + +
192A TYR* 4.9 4.5 - + - -
204A ILE 4.3 8.7 - - - -
205A ASN* 5.4 2.5 - - - -
206A PRO* 3.8 35.7 - - + -
207A LEU* 4.5 9.6 - - + -
209A PHE* 3.9 40.1 - + + -
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Residues in contact with ALA 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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90A THR 3.1 17.4 + - - +
91A ARG* 3.7 4.9 - - - +
93A PHE* 1.3 75.2 - - - +
95A SER* 1.3 65.0 + - - +
97A TYR* 3.1 3.6 + - - +
98A VAL* 3.0 27.7 + - - +
156A ILE* 4.7 2.9 - - + -
164A ILE* 4.1 25.8 - - + -
166A VAL* 4.4 6.7 - - + -
188A LEU* 4.0 24.9 - - + -
209A PHE* 3.9 4.9 - - + -
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG 2.9 18.0 + - - -
92A TYR* 3.6 6.3 + - - -
94A ALA* 1.3 76.2 - - - +
96A GLN* 1.3 58.4 + - - +
98A VAL* 3.4 1.1 + - - +
99A ARG* 2.9 48.2 + - - +
153A ILE* 4.2 17.2 - - - +
156A ILE* 3.8 17.8 - - - +
166A VAL* 5.3 0.2 - - - -
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Residues in contact with GLN 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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92A TYR* 3.1 55.5 + - + +
93A PHE* 3.5 22.9 - - + +
95A SER* 1.3 76.6 + - - +
97A TYR* 1.3 65.7 + - - +
99A ARG* 3.4 5.8 + - - +
100A ALA* 2.9 27.6 + - - +
115A LEU* 3.5 32.3 - - + +
119A LEU* 4.9 1.5 - - + +
204A ILE 5.1 2.9 - - - +
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Residues in contact with TYR 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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93A PHE 2.8 20.8 + - - +
94A ALA* 3.4 8.7 - - - +
96A GLN* 1.3 75.7 - - - +
98A VAL* 1.3 58.4 + - - +
100A ALA* 3.8 1.4 - - - +
101A ARG* 2.8 69.7 + - - +
115A LEU* 4.8 6.5 - - + +
116A VAL* 3.5 22.9 - - + +
119A LEU* 3.7 30.9 - - + +
120A SER* 2.6 31.4 + - - -
124A GLU* 4.0 1.0 - - - +
188A LEU* 4.2 6.7 - - + -
209A PHE* 4.7 2.5 - - + -
211A VAL* 3.8 27.4 - - + +
214A TYR* 3.8 27.8 - + - -
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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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94A ALA 3.0 16.2 + - - +
95A SER 4.1 2.5 - - - +
97A TYR* 1.3 76.4 - - - +
99A ARG* 1.3 56.4 + - - +
101A ARG* 4.6 1.1 - - - -
102A GLU* 2.9 44.0 + - + +
151A VAL* 4.7 3.4 - - + -
153A ILE* 4.8 0.9 - - + -
166A VAL* 3.9 30.3 - - + -
168A TYR* 3.6 40.2 - - + -
186A SER* 4.2 1.3 - - - +
188A LEU* 4.2 17.9 - - + -
214A TYR* 4.0 12.1 - - + +
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Residues in contact with ARG 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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95A SER* 2.9 34.4 + - - +
96A GLN* 3.9 5.2 - - - +
98A VAL* 1.3 74.3 - - - +
100A ALA* 1.3 62.6 + - - +
103A GLY* 3.3 21.3 + - - -
150A THR* 3.7 18.2 - - - +
151A VAL* 3.1 49.1 + - + +
152A THR* 5.1 0.6 - - - +
153A ILE* 4.3 12.7 - - + +
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Residues in contact with ALA 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 GLN 2.9 18.0 + - - +
97A TYR 3.8 2.2 - - - +
99A ARG* 1.3 80.7 - - - +
101A ARG* 1.3 62.1 + - - +
103A GLY 3.6 12.0 - - - +
112A SER* 3.8 35.5 + - - +
115A LEU* 4.2 18.2 - - + -
116A VAL* 3.9 15.8 - - + +
132A TYR* 5.9 2.9 - - - -
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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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97A TYR* 2.8 64.0 + - - +
98A VAL* 4.1 2.2 - - - +
100A ALA* 1.3 80.2 - - - +
102A GLU* 1.3 68.1 + - + +
103A GLY 3.8 3.8 + - - +
116A VAL* 3.8 13.0 - - + -
124A GLU* 2.9 28.1 + - - +
127A ARG* 5.3 1.2 - - - +
128A PHE* 3.8 48.8 - - + +
131A TRP* 3.8 31.7 - - + +
132A TYR* 5.7 2.3 - - - -
140A PRO* 4.2 4.5 - - - +
214A TYR* 3.4 35.5 + - - +
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Residues in contact with GLU 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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98A VAL* 2.9 22.2 + - + +
101A ARG* 1.3 86.9 + - + +
103A GLY* 1.3 59.1 + - - +
131A TRP* 4.5 14.2 - - - -
140A PRO* 5.8 1.6 - - - -
144A TYR* 4.5 6.3 - - - -
151A VAL* 3.8 12.8 - - + -
168A TYR* 3.3 25.1 + - + +
170A LYS* 3.4 41.5 + - - +
184A TRP* 6.0 0.3 - - - -
214A TYR* 2.6 43.6 + - + +
216A SER* 3.5 10.4 + - - -
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Residues in contact with GLY 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 ARG 3.3 17.8 + - - -
100A ALA 3.6 13.3 - - - +
101A ARG 4.1 3.6 - - - +
102A GLU* 1.3 80.4 - - - +
104A PHE* 1.3 67.5 + - - +
112A SER* 5.7 1.0 + - - -
132A TYR* 5.9 1.6 - - - -
140A PRO* 4.5 5.2 - - - +
144A TYR* 5.2 0.4 - - - -
149A ALA* 3.6 15.3 - - - -
151A VAL* 3.7 9.5 - - - +
170A LYS* 5.3 0.2 - - - -
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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