Contacts of the strand formed by residues 94 - 103 (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 THR 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D THR* 4.1 20.4 - - + -
11D SER 3.3 12.3 - - - +
12D VAL* 4.2 13.0 - - + +
93D HIS* 1.3 80.0 + - - +
95D VAL* 1.3 65.8 + - - +
96D GLN* 4.1 17.6 + - - +
117D ALA 3.9 0.2 - - - +
118D TYR* 3.5 7.7 - - - -
119D ASP* 2.8 38.0 + - - -
304D EDO 4.6 2.9 + - - -
31E HIS* 4.4 19.2 - - + -
32E PRO* 4.5 12.4 - - + +
33E SER* 5.6 0.8 + - - +
62E PHE* 4.6 3.4 - - + -
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Residues in contact with VAL 95 (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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9D PHE 4.0 0.2 - - - +
10D THR* 3.5 2.3 - - - -
11D SER* 2.9 35.4 + - - +
74D HIS* 4.1 24.5 - - + +
77D ASP* 4.6 9.0 - - + -
78D LEU* 3.3 40.6 - - + +
81D LEU* 4.6 6.3 - - + -
94D THR* 1.3 75.8 - - - +
96D GLN* 1.3 64.0 + - - +
116D TYR* 3.9 25.8 - - + -
117D ALA 3.6 6.1 - - - +
118D TYR* 4.2 11.7 - - + -
9F LEU* 4.9 3.8 - - + -
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Residues in contact with GLN 96 (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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9D PHE 3.2 10.5 - - - +
10D THR* 4.2 9.2 - - + +
74D HIS* 4.6 0.4 - - - -
94D THR* 4.1 10.0 - - + +
95D VAL* 1.3 82.0 - - - +
97D ARG* 1.3 61.5 + - - +
116D TYR* 3.1 9.0 - - - +
117D ALA* 2.9 35.5 + - + +
120D GLY 4.1 8.1 + - - -
31E HIS* 2.9 27.8 + - - -
56E PHE* 3.4 26.1 - - + -
60E TRP* 3.0 47.8 + - + +
62E PHE* 3.7 10.5 - - - -
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Residues in contact with ARG 97 (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* 3.5 0.9 - - - -
9D PHE* 2.8 43.7 + - + -
70D HIS* 3.9 21.9 + - - +
73D THR* 2.9 29.1 + - - +
74D HIS* 3.2 28.7 + - + +
96D GLN* 1.3 75.9 - - - +
98D MET* 1.3 66.8 + - - +
99D TYR* 4.0 12.3 - - - -
114D HIS* 4.0 21.0 - - + -
115D GLN 3.3 12.3 - - - +
116D TYR* 2.8 39.1 + - + -
56E PHE* 3.5 4.9 - - - -
60E TRP* 4.4 0.4 - - - -
5F PHE* 4.1 27.3 + - - +
7F HIS* 4.3 7.5 + - - +
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Residues in contact with MET 98 (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 40.2 - - + +
7D TYR 3.1 11.0 - - - +
8D PHE* 3.7 26.0 - - + -
9D PHE* 4.7 0.2 - - - -
97D ARG* 1.3 76.7 - - - +
99D TYR* 1.3 73.3 + - - +
113D TYR* 3.9 22.7 - - + -
114D HIS* 3.5 0.2 - - - -
115D GLN* 3.0 54.1 + - + +
56E PHE* 4.2 3.8 - - + -
58E LYS* 6.5 0.9 - - - -
60E TRP* 4.3 6.4 - - + -
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Residues in contact with TYR 99 (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 3.3 - - - +
7D TYR* 2.8 44.6 + + + +
9D PHE* 3.6 25.1 - + - -
70D HIS* 2.8 28.7 - + - -
97D ARG* 4.0 9.6 - - - -
98D MET* 1.3 81.4 - - - +
100D GLY* 1.3 58.1 + - - +
113D TYR 3.2 15.7 - - - +
114D HIS* 3.5 28.7 - + + +
159D TYR* 3.5 41.7 - + - -
160D LEU* 5.0 2.2 - - + -
2F LEU* 3.4 7.6 - - - +
3F GLY 3.2 14.9 + - - -
5F PHE* 3.7 20.9 - + + -
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Residues in contact with GLY 100 (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* 3.1 15.0 - - - -
6D ARG* 4.1 9.0 - - - -
7D TYR* 5.9 1.1 - - - -
99D TYR* 1.3 82.4 - - - +
101D CYS* 1.3 59.4 + - - -
112D GLY* 3.6 0.3 - - - -
113D TYR* 3.0 30.0 + - - +
159D TYR* 5.8 0.2 - - - -
160D LEU* 3.3 12.5 - - - +
164D CYS* 3.9 8.3 - - - -
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Residues in contact with CYS 101 (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* 3.3 0.5 - - - -
5D MET* 3.0 29.8 + - - -
6D ARG* 3.4 1.9 + - - +
100D GLY* 1.3 74.3 - - - +
102D ASP* 1.3 69.5 + - - +
109D PHE* 4.4 6.3 - - + -
111D ARG 3.4 9.9 - - - +
160D LEU* 3.8 16.2 - - + +
164D CYS* 2.1 57.9 - - - -
165D VAL* 3.7 10.1 - - + -
168D LEU* 4.4 11.7 - - - +
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Residues in contact with ASP 102 (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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2D SER* 6.1 1.1 - - - -
3D HIS 3.4 6.1 - - - +
4D SER* 3.1 10.9 - - - -
6D ARG* 2.6 38.5 + - - -
101D CYS* 1.3 73.4 - - - +
103D VAL* 1.3 68.2 + - - +
109D PHE* 3.8 1.7 - - - -
110D LEU* 2.9 37.0 + - + -
111D ARG* 2.9 18.4 + - + +
113D TYR* 3.0 27.3 + - - -
168D LEU* 5.0 0.2 - - - -
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Residues in contact with VAL 103 (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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2D SER* 3.3 5.4 - - - -
3D HIS* 2.9 46.4 + - + +
101D CYS* 5.4 0.4 - - - -
102D ASP* 1.3 80.3 - - - +
104D GLY* 1.3 68.5 - - - +
107D TRP* 3.7 28.3 - - + +
108D ARG 3.2 19.5 - - - +
109D PHE* 4.2 3.6 - - - -
110D LEU* 3.6 5.9 - - - +
165D VAL* 4.2 17.9 - - + -
168D LEU* 3.7 28.0 - - + -
169D ARG* 6.1 2.2 - - + -
172D LEU* 5.0 2.7 - - + -
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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