Contacts of the strand formed by residues 14 - 20 (chain D) in PDB entry 3RMD
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 SER 14 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D GLN* 3.7 2.3 - - - +
11D ILE 2.9 35.9 + - - +
12D GLY 3.1 1.8 - - - -
13D ASP* 1.3 83.7 + - - +
15D ILE* 1.3 62.3 + - - +
16D PHE* 3.6 14.9 - - - -
30D GLU* 4.0 17.3 + - - -
31D VAL 3.3 4.3 - - - -
32D GLU* 2.8 27.2 + - - +
65D MET* 3.9 0.7 - - - -
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Residues in contact with ILE 15 (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 VAL* 5.3 3.1 - - + -
9D GLU 3.1 9.4 - - - +
10D GLN* 3.7 17.3 - - + -
14D SER* 1.3 73.4 - - - +
16D PHE* 1.3 59.8 + - - +
17D GLU* 4.5 9.0 - - + -
29D ARG 3.7 0.5 - - - +
30D GLU* 3.6 2.9 - - - -
31D VAL* 2.8 57.0 + - + +
33D TYR* 4.2 5.4 - - + -
65D MET* 3.2 26.0 - - + -
89D LYS* 5.1 9.0 - - + +
92D TYR* 3.3 56.8 - - + -
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Residues in contact with PHE 16 (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 THR 3.7 1.4 - - - +
8D VAL* 3.4 2.7 - - - -
9D GLU* 2.7 38.0 + - + +
11D ILE* 3.4 47.3 - - + -
14D SER* 3.6 16.8 - - - -
15D ILE* 1.3 75.3 - - - +
17D GLU* 1.3 60.6 + - - +
28D THR* 6.0 1.6 - - + -
29D ARG 3.6 4.9 - - - +
30D GLU* 3.4 44.2 - - + -
245D HIS* 3.0 44.9 + + + +
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Residues in contact with GLU 17 (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 TYR* 3.7 3.3 - - + +
7D THR 3.3 3.1 - - - -
8D VAL* 3.8 18.8 - - + -
15D ILE* 4.0 4.0 + - + -
16D PHE* 1.3 73.7 - - - +
18D ARG* 1.3 74.3 + - - +
19D TYR* 3.4 7.6 - - + +
28D THR* 3.3 6.6 - - - +
29D ARG* 2.7 59.7 + - + +
92D TYR* 2.6 40.6 + - + -
97D TYR* 2.4 35.5 + - - -
245D HIS* 4.8 0.2 + - - -
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Residues in contact with ARG 18 (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 LEU* 2.6 40.0 + - + -
7D THR* 2.8 31.2 + - - +
17D GLU* 1.3 76.9 - - - +
19D TYR* 1.3 58.0 + - - +
26D GLU* 3.2 24.7 + - - +
27D ARG 3.4 7.0 - - - +
28D THR* 4.2 17.2 + - + +
209D THR* 3.3 32.4 + - - +
210D PRO 3.1 19.5 + - - -
211D VAL* 3.5 17.7 - - - +
244D PRO* 3.4 29.7 - - - +
245D HIS* 4.4 6.1 - - + -
267D GLY* 3.0 21.0 + - - -
268D ILE* 3.4 4.2 - - - +
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Residues in contact with TYR 19 (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 GLU* 3.3 33.7 - - - -
4D PHE 3.4 13.0 - - - +
5D TYR* 3.7 0.9 - - - -
6D LEU* 3.8 7.0 - - - +
17D GLU* 3.4 22.0 - - - +
18D ARG* 1.3 77.1 - - - +
20D ILE* 1.3 68.3 + - - +
21D ASP* 4.3 2.2 - - + -
26D GLU* 3.3 5.9 - - - +
27D ARG* 2.8 75.8 + - + +
28D THR 3.8 1.6 + - - -
29D ARG* 3.1 57.4 + - + +
97D TYR* 3.6 2.5 - - - +
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Residues in contact with ILE 20 (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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1D MET* 4.7 3.6 - - - -
3D GLU* 2.7 29.4 - - - +
4D PHE* 2.8 61.8 + - + -
6D LEU* 3.9 20.2 - - + -
19D TYR* 1.3 78.6 - - - +
21D ASP* 1.3 57.6 + - - +
24D GLY* 3.6 28.7 - - - +
25D ARG 3.6 1.1 - - - -
26D GLU* 4.0 18.2 - - + +
107D LYS* 3.6 32.1 - - + +
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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