Contacts of the strand formed by residues 3236 - 3249 (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 ASN3236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3232A LYS* 3.2 5.5 - - - +
3233A GLU* 2.7 51.1 + - + +
3235A GLU* 1.3 87.0 - - - +
3237A VAL* 1.3 65.7 + - - +
3238A VAL* 3.7 4.7 - - + +
4256A LYS* 6.3 2.4 - - - +
1286D LYS* 5.7 3.0 + - - +
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Residues in contact with VAL3237 (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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3227A ARG* 4.0 9.4 - - - +
3230A ALA* 4.0 10.5 - - + -
3231A VAL 3.7 2.9 - - - -
3232A LYS* 4.2 16.8 - - + -
3235A GLU 3.9 3.6 + - - +
3236A ASN* 1.3 75.1 - - - +
3238A VAL* 1.3 60.4 + - - +
3239A GLY 3.9 16.8 - - - +
3264A TYR* 3.8 14.6 - - + -
4253A ALA* 5.1 3.5 - - - +
4254A PRO 4.4 6.1 - - - +
4255A PHE* 3.7 46.0 + - + +
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Residues in contact with VAL3238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3231A VAL* 2.9 31.9 + - + +
3232A LYS 4.7 0.7 - - - +
3233A GLU* 3.9 30.3 - - + -
3236A ASN* 3.6 4.6 + - + -
3237A VAL* 1.3 72.7 - - - +
3239A GLY* 1.3 57.7 + - - +
3263A LEU* 3.8 12.3 - - + +
3264A TYR* 3.1 33.8 + - + +
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Residues in contact with GLY3239 (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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3227A ARG* 4.0 0.2 + - - -
3230A ALA* 3.7 4.5 - - - -
3231A VAL* 2.8 39.0 + - - +
3237A VAL* 3.9 4.0 - - - +
3238A VAL* 1.3 80.9 - - - +
3240A SER* 1.3 57.8 + - - -
3262A ILE 3.1 13.7 - - - -
3263A LEU* 4.1 2.5 - - - -
3264A TYR* 3.5 20.1 + - - -
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Residues in contact with SER3240 (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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3069A SER 4.9 1.4 + - - -
3070A SER 5.7 1.8 - - - -
3227A ARG* 3.0 28.7 + - - +
3229A GLY 3.7 3.8 - - - -
3231A VAL* 4.0 2.9 - - - +
3239A GLY* 1.3 70.8 - - - -
3241A GLU* 1.3 61.1 + - - +
3242A THR* 3.4 11.2 + - - -
3261A GLN* 3.6 1.2 - - - -
3262A ILE* 2.8 44.2 + - - -
3264A TYR* 2.7 25.7 + - - -
3502A ADP 3.5 13.6 + - - -
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Residues in contact with GLU3241 (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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3227A ARG* 3.6 4.2 - - - -
3228A ILE* 2.8 43.4 + - + -
3229A GLY* 2.8 31.5 + - - +
3230A ALA 4.4 3.7 - - - +
3231A VAL* 3.4 13.4 - - + +
3240A SER* 1.3 70.4 - - - +
3242A THR* 1.3 59.8 + - - +
3259A GLU* 5.6 2.8 - - + +
3260A PHE* 3.8 10.0 + - - +
3261A GLN* 3.2 39.3 + - - +
1232D LYS* 5.4 7.2 + - - +
1234D GLY* 4.1 24.7 - - - +
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Residues in contact with THR3242 (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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3070A SER 4.2 5.2 + - - +
3225A ILE* 3.7 28.3 - - + -
3226A ARG 3.6 6.6 + - - +
3227A ARG* 4.8 1.0 - - - -
3228A ILE* 4.4 3.4 - - - +
3240A SER* 3.4 14.4 + - - -
3241A GLU* 1.3 78.3 + - - +
3243A ARG* 1.3 64.7 + - - +
3258A ALA 3.9 0.4 - - - +
3259A GLU* 3.2 6.4 - - - +
3260A PHE* 2.7 74.7 + - + +
3262A ILE* 3.7 14.3 - - + +
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Residues in contact with ARG3243 (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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3224A ASP 3.6 2.1 - - - +
3225A ILE* 3.5 0.9 - - - -
3226A ARG* 2.9 39.3 + - + +
3228A ILE* 3.6 40.2 - - + +
3242A THR* 1.3 75.0 - - - +
3244A VAL* 1.3 65.9 + - - +
3245A LYS* 4.1 21.7 - - - +
3257A GLN* 3.3 30.7 + - - +
3258A ALA 3.3 5.2 - - - +
3259A GLU* 2.4 44.1 + - + -
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Residues in contact with VAL3244 (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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3047A LEU* 4.3 20.6 - - + -
3075A LEU* 4.3 6.5 - - + -
3223A LEU* 3.6 36.3 - - + -
3224A ASP 3.3 7.0 - - - +
3225A ILE* 3.8 21.8 - - + -
3243A ARG* 1.3 76.5 - - - +
3245A LYS* 1.3 64.8 + - - +
3246A VAL* 5.2 1.4 - - - +
3257A GLN* 3.3 5.0 - - - +
3258A ALA* 2.7 37.6 + - + +
3260A PHE* 3.7 31.0 - - + -
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Residues in contact with LYS3245 (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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3223A LEU* 3.5 4.0 - - - -
3224A ASP* 2.8 52.0 + - + +
3226A ARG* 5.9 5.1 - - - +
3243A ARG* 4.1 18.4 - - - +
3244A VAL* 1.3 74.0 - - - +
3246A VAL* 1.3 63.5 + - - +
3247A VAL* 3.3 12.6 + - + -
3255A PHE* 6.0 5.4 - - + +
3256A LYS 4.0 3.6 - - - +
3257A GLN* 3.5 33.9 - - + +
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Residues in contact with VAL3246 (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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3047A LEU* 4.3 9.0 - - + -
3050A ALA* 4.1 28.5 - - + +
3051A LEU* 4.4 7.0 - - + +
3222A ARG 3.7 5.2 - - - +
3223A LEU* 4.0 18.4 - - + -
3244A VAL 5.2 0.9 - - - +
3245A LYS* 1.3 71.6 - - - +
3247A VAL* 1.3 60.2 + - - +
3248A LYS 3.6 19.5 - - - +
3249A ASN* 3.9 26.5 - - + +
3254A PRO* 3.9 2.9 - - + -
3255A PHE* 2.7 37.0 + - - +
3256A LYS 3.0 21.7 + - - +
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Residues in contact with VAL3247 (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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2069A SER* 6.0 0.5 - - - -
3065A TYR* 3.5 27.1 - - + +
3222A ARG* 2.8 30.1 + - + +
3224A ASP* 3.5 24.5 - - + +
3245A LYS* 3.9 13.2 - - + +
3246A VAL* 1.3 74.5 - - - +
3248A LYS* 1.3 59.9 + - + +
3254A PRO* 4.6 1.9 - - - +
3255A PHE* 3.5 30.9 - - + -
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Residues in contact with LYS3248 (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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2068A GLU* 3.9 6.4 - - + +
2069A SER* 3.2 26.9 - - - +
2501A ALF 2.8 28.7 - - - -
2502A ADP 5.7 0.2 - - - -
3216A LYS 2.6 28.4 + - - +
3217A PHE* 2.8 24.9 + - - +
3219A ALA 3.0 20.3 + - - +
3220A SER 4.8 1.6 - - - +
3221A VAL* 3.2 6.0 - - - -
3222A ARG* 2.9 46.9 + - + +
3246A VAL* 3.6 8.1 - - - +
3247A VAL* 1.3 81.4 - - + +
3249A ASN* 1.3 68.2 + - - +
3250A LYS* 4.5 7.6 - - - -
3254A PRO* 4.4 2.0 - - - -
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Residues in contact with ASN3249 (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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2069A SER* 5.4 0.2 - - - -
2502A ADP 3.1 26.8 + - - -
3051A LEU* 3.2 27.5 + - - +
3220A SER 3.5 2.5 - - - -
3221A VAL* 3.7 9.8 - - - +
3246A VAL* 3.9 12.5 - - + +
3248A LYS* 1.3 80.5 - - - +
3250A LYS* 1.3 60.0 + - - +
3251A ILE* 3.0 27.9 + - - +
3252A ALA* 3.1 31.3 + - - +
3253A ALA 3.3 12.3 + - - -
3254A PRO* 3.8 19.1 - - + +
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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