Contacts of the strand formed by residues 20 - 28 (chain K) in PDB entry 5D4D
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 TYR 20 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14K ARG 5.7 0.7 - - - -
15K THR* 3.9 4.2 - - - +
16K GLN* 3.2 57.0 + - + +
17K GLY 4.2 2.8 - - - +
19K GLU* 1.3 80.9 - - + +
21K GLY* 1.3 76.5 + - - +
22K GLU* 2.8 46.4 + - + +
198K ARG* 3.2 24.4 + - + -
199K ILE 3.4 14.1 - - - -
200K TRP* 3.5 51.8 - + + +
207K PRO* 3.3 10.6 - - - +
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Residues in contact with GLY 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K ARG 3.4 11.0 - - - -
15K THR* 4.6 1.6 - - - -
20K TYR* 1.3 83.3 - - - +
22K GLU* 1.3 64.3 + - - -
23K PHE* 3.6 19.3 - - - -
197K LEU 3.7 0.3 - - - +
198K ARG* 3.5 3.1 - - - -
199K ILE 2.9 33.7 + - - -
207K PRO* 3.5 3.1 - - - +
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Residues in contact with GLU 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K THR 4.7 0.2 - - - -
13K VAL* 3.6 1.6 - - - -
14K ARG* 2.9 78.7 + - + +
20K TYR* 2.8 40.5 + - + +
21K GLY* 1.3 71.0 - - - -
23K PHE* 1.3 66.7 + - - +
24K VAL* 4.2 2.2 - - - +
196K THR* 4.8 5.2 - - + -
197K LEU 3.3 6.1 - - - +
198K ARG* 4.4 2.0 + - - -
932M GLU* 4.3 8.5 - - - +
934M PHE* 3.4 28.2 - - + -
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Residues in contact with PHE 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PHE* 4.2 9.2 - + + -
12K THR 3.5 3.4 - - - -
13K VAL* 3.9 28.5 - - + -
15K THR* 5.2 2.9 - - + -
21K GLY* 3.6 25.6 - - - -
22K GLU* 1.3 78.0 - - - +
24K VAL* 1.3 62.9 + - - +
25K LEU* 5.5 0.2 - - - +
195K LEU* 3.6 2.1 - - - +
196K THR* 3.5 1.5 - - - +
197K LEU* 2.9 51.6 + - + +
199K ILE* 4.3 13.2 - - + -
207K PRO* 3.7 15.3 - - + -
208K LEU* 3.4 51.8 - - + -
211K LEU* 3.6 28.0 - - + -
225L PHE* 5.3 3.1 - - + -
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K VAL 4.3 0.7 - - - -
11K PHE* 3.3 12.3 - - - -
12K THR* 2.9 49.5 + - - +
14K ARG* 3.4 34.8 - - + +
22K GLU 4.9 1.3 - - - +
23K PHE* 1.3 77.8 - - - +
25K LEU* 1.3 67.2 + - - +
26K GLU* 4.2 8.5 - - + +
194K LYS* 3.7 33.0 - - + -
195K LEU 3.3 9.4 - - - +
196K THR* 3.7 11.7 - - + +
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Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K PRO* 4.2 11.7 - - + -
10K VAL 3.5 3.1 - - - +
11K PHE* 3.4 32.1 - - + +
24K VAL* 1.3 73.3 - - - +
26K GLU* 1.3 60.1 + - - +
28K LEU* 3.8 30.3 - - + +
36K LEU* 4.0 9.0 - - + -
194K LYS* 3.9 0.7 - - - -
195K LEU* 2.9 39.7 + - + +
224L TYR* 3.3 39.0 - - + +
225L PHE* 3.7 33.0 - - + -
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Residues in contact with GLU 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K PRO* 3.5 4.2 - - - +
10K VAL* 2.9 52.8 + - + +
12K THR* 5.6 3.5 + - - +
24K VAL* 4.7 7.1 - - + +
25K LEU* 1.3 76.3 - - - +
27K PRO* 1.3 75.6 - - + +
28K LEU 4.2 0.2 - - - +
184K THR* 3.0 25.3 + - + +
194K LYS* 3.8 36.6 + - + +
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Residues in contact with PRO 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 3.6 25.2 - - + +
9K PRO* 3.3 23.9 - - + +
10K VAL* 5.0 3.6 - - + +
26K GLU* 1.3 89.3 - - + +
28K LEU* 1.3 60.8 + - - +
184K THR* 3.6 20.9 - - + -
185K ARG 5.4 0.9 - - - +
186K LEU* 4.1 31.0 - - + -
192K LEU* 3.8 15.9 - - + -
193K ASP 3.8 2.7 - - - +
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Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 5.0 3.1 - - - -
9K PRO* 3.9 22.7 - - + -
25K LEU* 3.8 28.9 - - + +
27K PRO* 1.3 74.8 - - - +
29K GLU* 1.3 62.2 + - - +
32K PHE* 4.1 23.6 - - + +
33K GLY 4.8 0.2 - - - +
36K LEU* 4.3 4.3 - - + -
192K LEU* 3.6 7.7 - - - +
193K ASP* 2.8 40.9 + - + +
195K LEU* 3.8 29.4 - - + -
221L HIS* 3.5 33.9 - - + +
224L TYR* 4.2 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