Contacts of the strand formed by residues 668 - 675 (chain D) in PDB entry 1MVW
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 HIS 668 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 6.2 0.6 - - - +
165D PHE* 4.5 22.5 - + - -
169D ASP* 4.7 5.1 + - - -
171D GLU* 4.2 17.2 + - - +
172D ASN 2.7 15.6 + - - +
173D GLN* 2.6 27.3 + - - +
174D SER 3.2 16.5 + - - -
494D HIS* 3.6 19.9 + + - -
498D LEU* 5.3 3.8 - - - +
667D THR* 1.3 69.1 - - - +
669D PRO* 1.3 85.3 + - + +
670D HIS* 3.3 24.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 669 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 5.5 2.4 - - - +
174D SER* 3.1 11.9 - - - +
176D LEU* 4.5 1.6 - - + -
490D PHE* 3.5 36.8 - - + -
494D HIS* 3.6 37.7 + - + +
667D THR 3.1 13.2 - - - +
668D HIS* 1.3 106.3 + - + +
670D HIS* 1.3 62.2 + - - +
671D PHE* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 670 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 6.2 1.8 - - - +
158D ILE* 4.5 18.0 + - + +
161D ASN* 5.2 3.3 - - + +
162D ALA* 4.1 13.6 - - + -
165D PHE* 3.9 23.1 - + - -
173D GLN* 3.2 34.1 + - + +
174D SER* 2.7 18.8 + - - +
175D ILE* 2.9 18.1 - - + -
176D LEU* 2.7 33.1 + - - +
668D HIS* 3.3 41.0 + + - -
669D PRO* 1.3 71.5 + - - +
671D PHE* 1.3 55.0 + - - +
672D VAL* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 671 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 3.7 19.6 + - + +
122D PHE* 3.7 22.7 - + + -
123D CYS* 3.5 18.2 + - - +
158D ILE* 4.4 4.4 - - - +
176D LEU* 3.9 25.1 - - + -
487D LEU* 4.8 3.8 - - + -
490D PHE* 4.1 7.9 - + - -
491D PHE* 3.2 56.3 - + + -
494D HIS* 4.2 15.5 - + - -
669D PRO* 3.7 30.1 - - + -
670D HIS* 1.3 71.8 - - - +
672D VAL* 1.3 68.5 + - - +
673D ARG* 3.9 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 672 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D CYS* 3.8 16.8 - - + +
125D THR* 4.9 1.6 - - - +
155D ILE* 4.5 25.4 - - + -
158D ILE* 4.2 20.4 - - + -
175D ILE* 3.8 22.7 - - + -
176D LEU 2.8 20.7 + - - +
177D ILE* 3.4 21.9 - - + -
178D THR 3.3 12.0 + - - -
188D ASN* 5.5 0.2 - - - +
192D VAL* 6.4 0.9 - - + -
671D PHE* 1.3 78.6 - - - +
673D ARG* 1.3 69.6 + - - +
674D CYS* 4.1 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 673 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PHE* 3.9 28.4 - - + -
123D CYS 3.3 11.8 + - - +
124D VAL* 3.4 4.9 - - - -
125D THR* 3.0 23.9 + - - -
176D LEU* 3.0 35.4 + - - +
178D THR* 3.6 30.6 + - - +
484D ASN* 5.4 2.6 + - - -
487D LEU* 5.1 15.4 - - - +
488D GLN* 4.6 8.9 + - - +
491D PHE* 5.9 1.8 - - - +
671D PHE* 3.9 21.8 - - - -
672D VAL* 1.3 77.5 + - - +
674D CYS* 1.3 62.5 + - - +
675D ILE* 3.9 5.7 + - + +
698D ASN* 3.2 50.9 + - + +
700D VAL* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 674 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D THR* 3.6 7.2 - - - +
177D ILE* 3.5 27.6 - - - -
178D THR 2.9 13.5 + - - +
179D GLY* 3.7 10.9 - - - -
183D ALA* 3.4 31.7 - - + +
185D LYS* 4.2 6.7 - - + -
188D ASN* 2.9 33.7 - - - +
672D VAL* 4.5 7.2 - - - -
673D ARG* 1.3 74.5 - - - +
675D ILE* 1.3 64.2 + - - +
694D GLN* 4.6 2.3 - - - +
698D ASN* 4.8 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 675 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 5.4 2.0 - - + -
124D VAL* 3.0 34.3 - - + -
125D THR 2.5 18.6 + - - +
126D VAL* 3.6 22.4 - - + -
127D ASN* 3.1 29.1 + - - +
183D ALA* 3.9 7.7 - - - +
673D ARG* 3.9 9.2 - - + +
674D CYS* 1.3 77.6 - - - +
676D ILE* 1.3 70.5 + - - +
677D PRO* 3.5 0.8 - - + +
691D VAL* 4.3 17.5 - - + -
694D GLN* 4.1 16.6 - - + +
695D LEU* 4.7 11.2 - - + -
698D ASN* 3.7 23.3 - - - +
700D VAL* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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