Contacts of the strand formed by residues 884 - 890 (chain A) in PDB entry 5C53
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 884 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A ILE* 3.6 31.0 - - + +
285A GLN* 5.6 0.7 + - - +
822A PRO* 4.2 11.0 - - + +
825A VAL* 3.5 26.0 - - + -
880A ALA* 3.8 6.8 - - + +
881A PRO* 2.9 43.1 + - + +
882A PRO 3.1 0.4 - - - -
883A GLY* 1.3 81.2 - - - +
885A THR* 1.3 64.0 + - - +
1126A ASP* 3.3 18.8 + - - -
1127A GLY* 5.3 2.7 - - - -
1140A LEU* 4.1 17.9 - - + -
1141A VAL 3.2 21.1 - - - +
1142A ARG* 2.9 42.1 + - + +
1143A GLU* 3.9 9.2 - - - +
1187A ARG* 4.9 2.1 + - - -
1209A ARG* 4.5 4.7 + - - -
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Residues in contact with THR 885 (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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880A ALA* 4.0 4.9 - - - -
884A TYR* 1.3 75.2 - - - +
886A LEU* 1.3 58.7 + - - +
887A VAL* 4.8 0.4 - - + -
1140A LEU* 4.2 3.6 - - - -
1141A VAL* 2.8 34.2 + - - +
1142A ARG 3.4 25.8 - - - +
1143A GLU* 3.6 13.0 - - + -
1146A ARG* 3.9 25.3 + - + +
1185A ILE* 4.2 3.0 - - + +
1186A ASP* 2.8 36.4 + - - -
1209A ARG* 4.0 10.6 + - - +
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Residues in contact with LEU 886 (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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436A PRO* 6.1 1.1 - - + -
878A VAL* 4.0 10.5 - - + +
880A ALA* 4.3 4.7 - - + +
885A THR* 1.3 73.9 + - - +
887A VAL* 1.3 60.3 + - - +
1131A ILE* 6.1 4.3 - - + -
1138A ARG* 4.2 19.7 - - + +
1139A TYR 3.3 12.6 - - - +
1140A LEU* 4.2 13.6 - - + +
1184A ASP 5.1 0.7 - - - +
1185A ILE* 3.4 2.6 - - - -
1186A ASP* 2.9 61.6 + - - +
1187A ARG 3.2 17.3 - - - +
1188A CYS 3.8 0.4 - - - +
1189A LEU* 3.5 46.4 - - + +
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Residues in contact with VAL 887 (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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885A THR* 4.5 1.8 - - + +
886A LEU* 1.3 76.3 - - - +
888A GLY* 1.3 60.2 + - - +
1138A ARG* 4.3 1.1 - - - -
1139A TYR* 2.9 35.2 + - - +
1141A VAL* 3.7 19.1 - - + -
1146A ARG* 3.7 23.1 - - + +
1149A ALA* 4.5 2.2 - - + -
1150A ALA* 3.9 15.7 - - + +
1153A LEU* 3.7 23.8 - - + +
1183A VAL* 3.8 7.2 - - + -
1184A ASP 3.3 2.9 - - - -
1185A ILE* 3.7 38.1 - - + -
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Residues in contact with GLY 888 (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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886A LEU* 4.2 0.4 - - - +
887A VAL* 1.3 74.8 - - - +
889A ALA* 1.3 63.1 + - - +
1137A VAL 3.1 14.1 - - - -
1138A ARG* 3.5 21.6 - - - +
1153A LEU* 3.9 5.4 - - - -
1183A VAL* 3.4 6.4 - - - +
1184A ASP* 2.9 34.0 + - - -
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Residues in contact with ALA 889 (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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888A GLY* 1.3 75.5 - - - +
890A ASP* 1.3 60.4 + - - +
891A VAL* 4.4 0.3 + - - +
1135A ASP 4.3 0.3 - - - +
1136A GLU* 3.2 6.8 - - - +
1137A VAL* 2.9 37.4 + - + +
1138A ARG* 4.0 2.0 - - - +
1153A LEU* 4.2 10.5 - - + +
1180A PHE* 3.6 38.3 - - + -
1182A ALA 3.8 13.7 - - - +
1183A VAL* 4.5 3.1 - - + -
1184A ASP* 4.9 2.7 - - - +
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Residues in contact with ASP 890 (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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889A ALA* 1.3 74.4 - - - +
891A VAL* 1.3 63.5 + - - +
892A ASP* 3.3 17.0 + - - +
1135A ASP* 3.0 20.9 - - - +
1136A GLU* 3.5 29.3 - - + +
1180A PHE* 4.0 8.2 - - - -
1182A ALA* 4.1 10.0 + - + +
1184A ASP* 5.6 1.7 + - - +
4002A MG 2.7 22.8 - - - -
4003A 4Y3 3.3 15.6 + - - -
101P DOC 5.7 2.1 - - - +
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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