Contacts of the strand formed by residues 4219 - 4233 (chain A) in PDB entry 3CMT
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 ALA4219 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4061A ILE* 3.3 14.8 - - - +
4063A GLU* 4.3 11.0 - - + +
4215A LEU* 2.9 21.9 + - + +
4216A LYS 4.2 1.1 - - - +
4217A PHE 3.6 0.7 - - - +
4218A TYR* 1.3 76.9 - - - +
4220A SER* 1.3 59.9 + - - +
4221A VAL 3.7 8.5 - - - +
4222A ARG* 3.7 28.7 - - + -
4248A LYS* 2.9 28.8 + - - -
4250A LYS* 4.1 1.9 - - - +
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Residues in contact with SER4220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3098A ALA* 4.7 2.6 - - - +
4057A PRO* 4.4 9.2 - - - -
4060A ARG* 3.0 52.5 + - - +
4061A ILE 2.7 12.2 + - - -
4218A TYR 3.4 5.9 + - - -
4219A ALA* 1.3 73.9 - - - +
4221A VAL* 1.3 63.0 - - - +
4248A LYS* 4.5 2.4 - - - +
4249A ASN* 3.5 2.3 + - - -
4250A LYS* 2.8 44.7 + - - +
4251A ILE* 4.5 1.5 + - - -
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Residues in contact with VAL4221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4051A LEU* 3.6 21.8 - - + -
4056A LEU* 4.1 8.5 - - + -
4057A PRO* 4.1 25.6 - - + -
4061A ILE 3.8 2.4 + - - -
4062A VAL* 3.4 15.9 - - + +
4063A GLU 3.0 23.4 + - - -
4219A ALA* 3.7 1.6 - - - +
4220A SER* 1.3 86.3 - - - +
4222A ARG* 1.3 68.8 + - - +
4223A LEU* 3.5 27.4 - - + -
4246A VAL* 4.7 1.1 - - + -
4248A LYS 3.2 8.5 - - - +
4249A ASN* 3.7 17.0 - - - +
4251A ILE* 4.8 3.6 - - + -
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Residues in contact with ARG4222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3068A GLU* 4.6 8.3 + - - -
4063A GLU* 2.4 50.7 + - + +
4065A TYR* 3.7 29.8 + - + -
4209A THR* 4.5 7.7 + - - +
4216A LYS* 4.0 44.8 + - - +
4219A ALA* 3.7 19.5 - - + -
4221A VAL* 1.3 78.4 - - - +
4223A LEU* 1.3 66.1 + - - +
4246A VAL 3.6 0.5 - - - -
4247A VAL* 2.8 42.7 + - + +
4248A LYS* 2.9 35.2 + - + +
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Residues in contact with LEU4223 (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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4047A LEU* 4.5 17.7 - - + -
4051A LEU* 4.3 4.3 - - + -
4056A LEU* 4.3 22.2 - - + -
4062A VAL* 4.6 2.0 - - + -
4063A GLU 2.7 11.9 + - - +
4064A ILE* 3.4 30.6 - - + +
4065A TYR* 2.8 35.0 + - - +
4075A LEU* 4.9 4.7 - - + -
4221A VAL* 3.5 20.0 - - + -
4222A ARG* 1.3 80.6 - - - +
4224A ASP* 1.3 59.6 + - - +
4225A ILE 3.8 0.4 - - - -
4244A VAL* 3.7 20.2 - - + -
4245A LYS 3.5 1.6 - - - +
4246A VAL* 4.0 25.4 - - + -
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Residues in contact with ASP4224 (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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4065A TYR* 3.5 30.5 + - + +
4207A GLU* 4.9 0.3 - - - +
4222A ARG 4.2 0.8 + - - -
4223A LEU* 1.3 70.5 - - - +
4225A ILE* 1.3 62.0 + - - +
4226A ARG* 2.7 41.4 + - - +
4243A ARG 3.6 1.6 - - - +
4244A VAL* 3.3 3.5 - - - -
4245A LYS* 2.8 47.9 + - + +
4247A VAL* 3.6 24.1 - - + +
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Residues in contact with ILE4225 (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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4064A ILE* 3.8 13.0 - - + -
4065A TYR 2.9 18.7 + - - +
4066A GLY* 3.4 2.6 - - - -
4067A PRO* 3.4 14.9 - - - +
4070A SER* 3.6 26.5 - - - +
4071A GLY* 3.8 19.3 - - - +
4072A LYS* 3.6 26.7 - - + -
4075A LEU* 4.0 15.5 - - + -
4223A LEU 3.8 0.8 - - - -
4224A ASP* 1.3 73.3 - - - +
4226A ARG* 1.3 73.0 + - - +
4242A THR* 3.8 22.4 - - + -
4243A ARG 3.5 2.7 - - - -
4244A VAL* 3.8 17.5 - - + +
4260A PHE* 4.6 0.9 - - + -
4262A ILE* 4.8 2.0 - - + -
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Residues in contact with ARG4226 (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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4065A TYR* 4.6 1.4 - - - -
4067A PRO* 3.4 25.0 - - + +
4070A SER* 4.2 9.0 - - - -
4195A ILE* 3.2 20.2 - - - +
4207A GLU* 2.7 39.7 + - - -
4224A ASP* 2.7 34.2 + - - -
4225A ILE* 1.3 81.0 - - - +
4227A ARG* 1.3 66.7 + - - +
4228A ILE* 3.6 9.5 + - + +
4242A THR* 3.5 2.6 - - - +
4243A ARG* 2.9 39.8 + - + +
4245A LYS* 5.9 5.4 - - - +
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Residues in contact with ARG4227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4067A PRO* 5.5 1.6 - - - +
4068A GLU 6.1 0.2 - - - +
4069A SER* 4.6 8.3 - - - +
4070A SER* 4.2 21.1 + - - +
4226A ARG* 1.3 74.4 - - - +
4228A ILE* 1.3 61.5 + - - +
4229A GLY* 3.6 26.4 + - - +
4230A ALA* 3.5 28.5 - - - +
4237A VAL* 4.1 7.1 - - - +
4239A GLY 4.0 1.2 + - - -
4240A SER* 3.0 23.4 + - - +
4241A GLU 3.6 7.4 - - - +
4242A THR* 4.7 2.9 - - - +
4264A TYR* 3.6 17.4 + - - -
4502A ADP 4.7 2.9 + - - -
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Residues in contact with ILE4228 (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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4226A ARG* 3.9 10.1 - - + +
4227A ARG* 1.3 77.4 - - - +
4229A GLY* 1.3 59.0 + - - +
4241A GLU* 2.8 37.9 + - + +
4242A THR 4.2 4.3 - - - +
4243A ARG* 3.6 56.5 - - + +
4259A GLU* 4.0 22.0 - - + +
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Residues in contact with GLY4229 (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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4227A ARG* 3.6 23.0 - - - +
4228A ILE* 1.3 82.1 - - - +
4230A ALA* 1.3 56.1 + - - -
4240A SER* 3.7 0.3 - - - -
4241A GLU* 2.8 36.7 + - - +
232D LYS* 5.9 4.9 - - - -
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Residues in contact with ALA4230 (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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4227A ARG* 3.5 24.0 - - - +
4229A GLY* 1.3 73.2 - - - -
4231A VAL* 1.3 63.1 + - - +
4232A LYS* 3.6 22.8 + - + +
4237A VAL* 4.0 17.9 - - + -
4239A GLY 3.7 0.2 - - - -
4241A GLU* 4.6 4.4 - - - +
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Residues in contact with VAL4231 (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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4230A ALA* 1.3 69.5 - - - +
4232A LYS* 1.3 63.2 + - - +
4237A VAL* 3.7 2.4 - - - -
4238A VAL* 2.9 43.4 + - + +
4239A GLY* 2.7 30.9 + - - +
4240A SER 4.0 1.3 - - - -
4241A GLU* 3.4 31.4 - - - +
4261A GLN* 3.5 31.0 - - + +
4263A LEU* 4.0 12.6 - - + -
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Residues in contact with LYS4232 (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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4230A ALA* 3.6 17.0 + - + +
4231A VAL* 1.3 81.6 - - - +
4233A GLU* 1.3 62.4 + - - +
4234A GLY 3.5 21.7 + - - +
4235A GLU 4.8 3.6 - - - +
4236A ASN 3.2 10.8 - - - +
4237A VAL* 4.2 17.3 - - + -
4238A VAL* 4.7 1.3 - - - -
230D ALA 5.8 2.2 + - - -
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Residues in contact with GLU4233 (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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4231A VAL 4.3 0.2 + - - -
4232A LYS* 1.3 71.6 - - - +
4234A GLY* 1.3 53.4 + - - +
4235A GLU* 2.7 16.3 + - - +
4236A ASN* 2.7 35.7 + - + +
4238A VAL* 3.9 25.4 - - + -
289D ALA* 4.6 17.3 - - - +
291D TYR* 5.6 2.3 + - - -
300D GLN* 6.1 0.3 - - - +
301D GLY* 3.8 26.1 - - - -
302D LYS* 4.5 7.1 + - - +
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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