Contacts of the strand formed by residues 3 - 12 (chain D) in PDB entry 5MEP
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 HIS 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D GLY* 3.1 34.0 + - - -
2D SER* 1.3 77.8 + - - +
4D SER* 1.3 62.3 + - - +
29D ASP* 2.7 33.0 - - - +
102D ASP* 3.4 4.3 - - - +
103D VAL* 2.9 38.4 + - + +
107D TRP* 3.9 26.1 + + - -
168D LEU* 4.4 3.6 - - + -
172D LEU* 3.7 33.9 - - + +
179D LEU 4.4 9.9 + - - -
180D GLN* 4.4 12.2 - - + +
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Residues in contact with SER 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D HIS* 1.3 74.0 - - - +
5D MET* 1.3 59.2 + - - +
6D ARG* 3.8 17.9 + - - +
28D VAL* 3.2 8.0 - - - +
29D ASP* 2.8 44.0 + - - +
101D CYS 3.3 6.3 - - - -
102D ASP* 3.1 25.1 - - - -
168D LEU* 4.1 6.5 - - - +
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Residues in contact with MET 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D SER* 1.3 73.8 - - - +
6D ARG* 1.3 69.0 + - - +
7D TYR* 4.2 29.8 - - + -
27D TYR 3.4 12.1 - - - +
28D VAL* 4.8 1.1 - - + -
33D PHE* 4.4 4.9 - - + -
100D GLY* 3.1 22.9 - - - -
101D CYS* 3.0 13.8 + - - +
159D TYR* 4.2 0.9 - - - +
164D CYS* 3.4 42.6 - - - +
167D TRP* 4.4 3.4 - - + -
168D LEU* 3.7 22.5 - - + +
171D TYR* 3.6 32.5 - - - -
1F ILE 4.2 12.3 - - - +
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Residues in contact with ARG 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D SER* 3.8 15.2 + - - +
5D MET* 1.3 77.4 + - - +
7D TYR* 1.3 63.9 + - - +
8D PHE* 3.5 24.5 - - + -
25D VAL 4.1 0.3 - - - +
26D GLY* 3.5 2.1 - - - -
27D TYR* 2.8 45.0 + - + +
29D ASP 5.9 0.4 - - - +
98D MET* 3.5 33.8 - - + +
99D TYR 3.5 5.6 - - - +
100D GLY* 4.3 2.0 - - - -
101D CYS 3.4 14.8 + - - +
102D ASP* 2.6 36.6 + - - -
113D TYR* 3.2 32.0 + - - -
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Residues in contact with TYR 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D MET* 4.2 16.6 - - + -
6D ARG* 1.3 74.8 - - - +
8D PHE* 1.3 61.4 + - - +
9D PHE* 3.7 21.7 - + + -
24D ALA* 6.5 0.2 - - + -
25D VAL 3.5 4.9 - - - -
26D GLY* 3.7 23.3 - - - -
33D PHE* 3.6 16.7 - + - -
34D VAL* 4.1 15.3 - - + -
45D MET* 5.3 1.6 - - + -
59D TYR* 4.7 1.0 + - - -
63D GLU* 4.3 2.5 + - - -
98D MET* 3.1 6.8 - - - +
99D TYR* 2.8 54.5 + + + +
100D GLY* 5.9 0.9 - - - -
159D TYR* 3.9 4.3 - - - -
171D TYR* 4.2 0.2 + - - -
1F ILE* 2.6 52.6 + - - -
2F LEU* 3.4 22.8 + - + -
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Residues in contact with PHE 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ARG* 3.5 29.4 - - + -
7D TYR* 1.3 74.5 - - - +
9D PHE* 1.3 64.7 + - - +
23D ILE 4.0 0.9 - - - +
24D ALA* 3.4 4.2 - - - +
25D VAL* 2.9 36.5 + - + +
27D TYR* 3.6 34.8 - + - -
97D ARG 3.5 3.1 - - - -
98D MET* 3.7 25.6 - - + -
55E SER* 4.1 14.4 - - - +
56E PHE* 3.3 56.3 - + + +
57E SER 5.4 2.9 - - - -
63E TYR* 5.6 1.1 - - - -
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Residues in contact with PHE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 3.7 25.8 - + + -
8D PHE* 1.3 73.0 - - - +
10D THR* 1.3 65.0 + - - +
22D PHE* 3.8 17.9 - + + -
23D ILE 3.6 3.8 - - - -
24D ALA* 3.7 25.1 - - + -
25D VAL 5.7 0.2 - - - -
67D VAL* 4.7 3.6 - - + -
70D HIS* 3.3 32.8 - + + -
74D HIS* 3.9 19.3 - - - +
96D GLN* 3.2 5.9 - - - -
97D ARG* 2.8 54.8 + - + +
99D TYR* 3.6 22.4 - + - -
56E PHE* 3.6 3.6 - - - -
2F LEU* 3.7 26.7 - - + -
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Residues in contact with THR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PHE 5.5 0.2 - - - -
9D PHE* 1.3 76.5 - - - +
11D SER* 1.3 61.0 + - - +
12D VAL* 4.1 13.0 - - + -
21D ARG 3.7 0.9 - - - +
22D PHE* 3.4 6.4 - - - -
23D ILE* 2.9 40.3 + - + +
74D HIS* 4.7 0.4 - - - -
94D THR* 4.1 15.9 - - + -
95D VAL 3.5 3.8 - - - -
96D GLN* 4.2 1.9 - - + +
54E LEU* 4.4 18.1 + - + +
56E PHE* 3.5 22.7 - - - -
62E PHE* 3.6 28.4 - - + -
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Residues in contact with SER 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 1.3 69.5 - - - +
12D VAL* 1.3 66.1 + - - +
20D PRO* 4.6 4.3 - - - +
21D ARG 3.1 7.8 + - - -
22D PHE* 3.3 18.5 - - - +
71D SER 4.7 1.4 + - - -
74D HIS* 3.2 37.1 - - - +
75D ARG 4.8 0.3 + - - -
78D LEU* 4.1 17.2 - - - +
93D HIS 3.9 0.3 - - - +
94D THR* 3.3 5.5 - - - +
95D VAL* 2.9 31.6 + - - +
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Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR* 4.1 14.8 - - + -
11D SER* 1.3 80.1 - - - +
13D SER* 1.3 74.6 + - - +
14D ARG* 3.8 2.9 - - - +
20D PRO* 3.2 6.2 - - - +
21D ARG* 2.9 42.0 + - + +
92D SER* 3.6 12.8 - - - +
93D HIS 3.4 7.2 - - - +
94D THR* 4.2 11.2 - - + +
304D EDO 3.8 18.4 - - - +
33E SER* 3.9 19.3 - - - +
54E LEU* 6.2 0.2 - - + -
101E EDO 4.2 11.9 - - - +
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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